Found this on a CJ specific forum and copied it over here. Sounds very helpful in my search for a CJ7.
Engine
Before AMC bought the Jeep corporation in the early '70s there was rarely a choice of engines. You usually got a four cylinder engine but from 1966 to 1971 some CJ5's and CJ6's came with the desirable Dauntless “Odd Fire” V6. This was a strong, reliable engine with plenty of low end torque. Click here for more info on the Dauntless V6
Unless high gas mileage is your goal you may want to avoid the 4 cylinder engines. The GM “Iron Duke” engine was a particularly weak 4 cylinder engine to avoid. The Iron Duke was found in CJs from 1980 to 1983. It can be identified because the intake is on one side of the engine and the exhaust is on the other. The more desirable AMC 4 cylinder engine has both the intake and the exhaust on the left side.
The AMC era saw some good engines. The 258 straight six has an excellent reputation as a strong, torquey, reliable motor.
If you are looking for a V8 the AMC 304 was offered from from 1972 to 1981.
Transmissions
The '70s saw some good strong transmissions but they were often 3 speeds. The best transmission to ever go into a CJ was the T18 four speed. It was available from 1971 to 1979. Many (but not all) T18 transmissions had a granny low first. Click here for more info on the T18 Transmission
In the '80s the three speeds were gone and overdrive was becoming common, but the '80s also saw some of the worst transmissions to go into CJs. If you are looking for CJ from the '80s try to get the T176 four speed.
The best automatic transmission to go into a CJ was the TH400. This transmission was available from 1976 to 1979 and it only came with the QuadraTrac transfer case.
Transfer Cases
Jeep CJ's have had some excellent transfer cases. The Dana 18, 20 and 300 were all good strong gear driven transfer cases.
The QuadraTrac transfer case was unique for many reasons. It was the only full time four wheel drive system offered in a CJ. It was the first chain driven transfer case. If the oil level was not always kept up the chain would stretch, possibly to the point of jumping teeth.
Frames
When you begin looking for your CJ, one place you really want to check is the frame itself. The newest CJ out there has seen 26 years of wear and tear and you want to make sure it has a solid foundation.
Rust
CJs have a few common rust areas that should be checked before purchase. The first area to check would be around the front and rear shackle mounts. Mud and dirt get in these areas and block the holes in the boxed frame models not allowing moisture to escape. Check them thoroughly with a hammer and screwdriver.
The next area to check would be the section located directly behind the rear wheels. Use the same method as described above. Also look at the 6 body mounts that attach the tub to the frame.
If your looking at a wide trac model ( 82-86 ) take note of the shock towers located in the front fenders. These held water between the frame and the tower itself and are another common rust area.
It is best to go over the entire frame if possible. Any area that could hold moisture in is a potential problem rust area and compromises the integrity of the frame.
Cracks
While your under your possible next project checking for rust, look for cracks in the frame as well.
On early "c" channel (non boxed) frames pay attention to the whole frame. These frames have most likely been put through quite a few "flex cycles" and warrant attention throughout the entire frame.
On later boxed frames ('76 and up) one of the most common areas to see cracks is around the steering box area. Take note of this area especially on CJs with lift kits and oversized tires.
Summary
The frame is the basic building block or "backbone" of your CJ. A rusted and or cracked frame has been the demise of many CJs over the years. When at all possible check the full frame thouroughly. The points where the suspension and steering mount are critical to the safety of your CJ and should warrant specific attention.
Body
The body is the first thing you see when looking at a potential CJ purchase. Conditions of the body of CJs will run the gammet. From full restoration beautys to ones with holes large enough to lose small children, your likely to see it all in your quest for a CJ.
You'll also run into dings, dents, overall damage and "modifications". You may see repairs made with chicken wire , bondo , aluminum tape and even that aerosol spray foam. It will be up to you to know your limitations when it comes to body repair.
Front Clip
The front clip is easily removed with common hand tools. The fenders , grill, and hood can all be removed with the turn of a few bolts in stock form. Look for rust on the inner fenders and bottom corner that meets the body tub.
Your candidate could also have a fiberglass front clip. These are either bolted on like their steel counterparts or are 1 piece with the fenders and hood molded together. Common things to be aware of with fiberglass are cracks and damaged gel coat.
When inspecting fiberglass look at all the areas where mounts or fasteners are used. This is a common place for damage. Also look for quality of the production of the fiberglass parts. There should be thicker reinforced areas at any mounting points.
When looking at a 1 piece fiberglass front end you will also have to look at the previous owners fabrication. Be wary of poorly mounted radiators and loose or draped wiring harnesses.
Windshield ,doors ,tailgate
The windshield frame is also a common rust area on CJs. Areas to take a good look at are right at the hinges and the top of the frame where screws have been used and holes have been drilled. If water has layed in the frame itself the bottom of the frame can easily rust out. This is often caused by the design of the defroster itself. Warm moist air is pumped through the frame itself causing condensation to rust the bottom of the frame. If you have the opportunity fold the windshield forward and check this area.
If your looking at a CJ with steel doors pay attention to the bottom area when looking for rust. Another problem on full steel doors is a stress crack developes right below the wing window. Also check for brittle and worn weatherstripping around the outside of the door and in the window areas.
Check the tailgate for rust around the weather stripping and for missing cables and / or hardware.
Body Tub
The body tub is where you'll spend all your driving time and should be paid close attention to. There are many common areas for rust on a CJ tub. The rocker area under the doors and the rear corners of the tub are 2 such areas. Many times these areas are shoddily patched or covered with diamond plate.
The body tub sees a lot of stress where the body mounts support the tub. With a little rust or abuse these body mounts can become damaged or press through the body.
Around the wheelwells and under the roll bar are also spots that deserve your attention. If the CJ your looking at has carpeting try and pull it back away from these areas to get a good look.
The entire floor area needs to be inspected as well. Mud, dirt and road salt (for those that live in areas that use it) wreak havoc on the underside of your CJ. Look for poorly replaced/patched floors as well. Patches that are put over rusted metal only become rusted metal themselves.
The last two areas to check are the cowl under the windshield frame and the tailgate area. These areas use weather stripping and a gasket. When either fails it usually holds water in causing rust. You can pop out the two plastic inserts on the inside of the windshield frame and inspect it somewhat using a flashlight.
Inspecting a CJ
One of the biggest things that should be done when looking at a CJ is to inspect for rust and bondo. Remember one of the biggest pains is bodywork. I go around the Jeep knocking every few inches all over with my knuckles. If the owner gets nervous I will walk off.
Next I'll go under the Jeep and inspect the frame. On the frame I'll use a pair of pliers or another tool I have available to find any rusted areas. Once I know the body and frame are sound I move on to the rest of the Jeep.
Remember the seller wants to show you the highlights of the Jeep and steer you from the possible problem areas. Don't get all enamored with showy items , just move on to areas you are interested in.
Project Jeeps
These are possibly the worst Jeeps you can buy. Usually someone selling a project Jeep has found out he is in over his head and has parts from here to Hells half acre (and yes hes lost some important ones) or has started the conversion and found its going to cost a small fortune to complete.
Most Jeeps bought in this condition end up going to a Junk yard or sold as parts Jeeps at a considerable loss. You have to have a backyard full of Jeep parts and and a lot of experience to completely reassemble a torn down Jeep.
Wiring a Jeep from scratch is not a chore for a person who has never worked with wiring before. Doing a engine or tranny conversion can get into thousands of dollars alone.
Remember when you change one item it will usually effect 10 others. Jeep projects are for the experienced rebuilder with a pile of Jeep parts in reserve.
Built Jeeps
Another thing to avoid is Jeeps built to the max. Most of this type have been beaten severely on the trail. With some the build is not what they wanted and trouble has arrived. Why else would he be selling something he has spent thousands on?
While he may just be needing money many times problems have arose that are too costly to fix. Built to the hilt Jeeps are rarely a nice thing.
Street Queens
This is the area you would like to find your Jeep in. With all the information other have written finding a Jeep that has spentmost of its life fairly stock will make a fine vehicle to buy.
Yes you can still do whatever modifications you'd like. Maybe you'd even want to do a full frame off restoration. This way you are going to find that the Jeep is easier to find parts for and not run into conversions that are extremely expensive to fix. Street Queens are the way to go when buying a Jeep.
Electrical
This is something that gets hours and hours of attention and discussion. At very best you have an electrical system that is 30 something years old and most have spent significant time in hostile and corrosive atmospheres. At the very worst one or more of the previous owners considered his stereo system to take priority over things as foolish as tail lights. The obvious conclusion is that the more pristine and original the wire is in the easier it is to keep everything running. As always be cautious of the seller who starts by telling about the killer system and/or the 8 day lighters that replaced the high beams.
Good indications of electrical challenges is the number of splices you see with duct tape insulation, before I get jumped on here there are a couple of these from the factory but these would hopefully be wrapped in convoluted tube. Wire nuts and "scotch locks" are a definite no-no. Look at the fuse block. fuses wrapped in tin foil and spent 22 shells are always a dead give away of possible problems. Soldered splices, when splices are necessary , are my first choice but not every body is talented with a soldering iron so if the lump under the heat shrink is a bit large it may be time to pull the pocket knife and take a closer look.
After market wire harnesses, are not magic or blessed from on high and when you are through you don't have the luxury of a factory diagram telling you what color what is and where it is supposed to start and end. If your buying a machine with a replacement harness you already know for a fact the PO has had his way with every wire in the entire system. Tell me that gives you a warm secure feeling.
Having taken all this into consideration, keep in mind that 80% of your problems will be electrical 10% will be vacuum leaks and the other 10% will be deciding what size tires to run and fun easy stuff like that. Of that 80%, half of those will be bad ground connections. Grounding failure is directly proportional to rust and corrosion. Keep this in mind as you are examining the body, it isn't just about looks.
There are enough threads on trouble shooting 12V DC electrical systems and proper use of a VOM that this is not the place to discuss it. As vehicle electrical systems go you are not going to find an easier system to understand or work on than the CJ. Do be prepared to spend some time with the electrical system and if you don't think you can ever get your head around a wiring diagram or be able to learn the difference between volts and ohms you may want to rethink this whole thing before you become the PO that the next guy blames for all the electrical problems.
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