Got the new setup dropped in today. It was a bit of a process by myself but not too bad. I was able to get the engine about halfway in and set it on a cross member after I put the jack under the tail of the transmission. After that I hooked the engine hoist to the front of the engine. This setup gave me more independent control of the front and rear heights.
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After a bit of jiggling and making adjustments I decided that it would be beneficial to remove the intake as it was hitting the firewall but I still needed to go up to get on the engine mounts. Once that was off it went into place fairly easily.
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Once the front was in I threw the transmission cross member back in and the jeep was freestanding again.
I'm going to ask MOTECH about the intake. I tried to set it back in the valley but it was hitting the firewall. After giving up on that and cleaning some things up I noticed the engine had come back a couple inches so I may be able to pull it forward and use that intake. Worst case I'll just get a LT1 intake like Moby and call it a day.
Anybody who has ordered an atlas, do they offer any other shipping if you call and make the order? I was looking online and they only offer 3 day shipping for $500.