How long have you had your SunCoast TC? I just had mine installed by SunCoast and the TC has a 2 year warranty which I assume applies regardless of who did the install.

Your position with respect to the F-37 is a bit odd and I'm not sure I fully understand the implications but my The F-37 is a recall not a TSB so I suspect there is some obligation on the part of the dealer to do the work even if you don't want it. IIRC the F-37 consisted of inspection and replacement, if necessary, of the TC and the ECU/TCM detune. You don't have an OEM TC so replacement would not be Jeep's obligation although I suppose it's possible that they cannot tell that your TC is not OEM (I have no clue if SunCoast marks their TCs but it would not surprise me) in which case you might get lucky and get Jeep to give you a new TC. If so that new TC will NOT be a Euro. However, IIRC there have been at least 1 or 2 folks who got a Euro installed as part of a late F-37 by paying for the part (the recall covered the labor). As for the flash I'd be pretty sure they will reflash the ECU (don't know Inmotions policy or price to reflash) but you may be able to talk them into "forgetting" to do the TCM shift point reflash. I know for a fact that some have been successful in haveing this part of the F-37 omitted (my 05 was one where it was omitted but I don't know how because I purchased the vehicle used).

So your best bet may be to see if you can prohibit the dealer from doing anything but the suspension recall and take it to a tranny shop to deal with the tranny issues.