I'm sorry to hear about your difficulties with the modifications to your Jeep and now the possible warranty issue. These things can be stressful, especially if you depend on your rig for regular transportation.
Reading between the lines, it seems the dealership isn't flatly denying to cover your transmission problem under warranty, but giving you fair warning that they might have to charge for some or all of the necessary repairs. In any event, after diagnostics, they should clearly communicate your out of pocket costs, giving you the choice to have it done somewhere else if you do not want to pay them for the repair.
I bought my JKU with the intention of doing a lot of modification, so I never expected any warranty, but I have been pleasantly surprised by how fairly the local dealer (who didn't sell me the JK) has been. All recall work has been done promptly and courteously; including some warranty work.
If I can offer anything other than empathy for your situation, which is far from unique, it would be to do your due diligence, deal with reputable outfits, communicate your expectations clearly and get it in writing. Colorado does not deal with fraudulent repair operations lightly, but you have to be able to document your case. I know of a transmission shop owner in Colorado Springs who went to jail for dishonest practices.
Good luck with your Jeep and let us know how things resolve.
-meljr
