I'm about to do an engine swap on the TJ to a 4.7l stroker and upgrading the turbocharger to a GT3582. The engine and turbo will be good for 5-600 hp give or take and the NV3550 that currently calls the trans tunnel home most likely will be overwhelmed along with the clutch. I have already ordered a Pro Series 4.3 Atlas that should start being built any day. The question I have is do I have it built for the 3550 knowing that I will probably change it out in the future, or do the auto swap now and have the Atlas setup for the auto and save having to do driveshafts and skid plate mods twice?? I think the Ford 6R80 is the trans I am most interested in running. It has a nice low 4:17 first gear and are known to hold huge hp stock. Guys are running these trans in Mustangs to over 1000 hp with little or no mods. Also Atlas has an option to setup the input for it as well, so with a phone call I should be able to get it done. The other huge benefit is the tuning. The AEM engine computer I am running would be able to handle the trans control and I could have options for convertor clutch lockup and paddle shift. Thoughts?? Pros - cons??