Thanks for the replies guys.
@Guardrail - Believe the output shaft sensor is in the lead frame. I've replace that assembly twice now, so fairly confident I've eliminated that possibility.
@New recaros and
@mprice1234 - I am unable to go back to stock tune as I have a whipple installed.
@FordTechOne - Thanks for the input and helping me eliminate that it's most likely not the tune.
@MTF - Good idea, I checked the harness and it is fine. Previous owner had the power commander set at the second to lowest setting. Obviously can't attest to where he might have had it before. Regardless, my issue now.
@BSouders80 - Could you elaborate on your last sentence? Quicker in the long run? Not happy with MS Racing?
@ThrillSeeker24 - Appreciate the input. I'm at a crossroad on either to rebuild it stronger, or purchase a reman with warranty. Both options are quite a bit of $$ especially compared to 5.0 6r80 I see out there.
@Gumby - Not too familiar with the Roush setups. Was yours supercharged originally when purchased? How has your transmission been holding up?
Again, appreciate all the input.
To be honest, I'm experiencing a little sticker shock all the way around. Whether its a reman from Ford (~5k installed), rebuild (~5.5k installed) or built (~6-9k not installed). Junk yards seem to be ~ 1,600 and up with high mileage. 5.0 6r80 transmissions are cheaper, and I've read where a few people claim they bolted up fine, but they are different part # so something has to be different.
Reman vs stock rebuild vs upgraded: My truck has 139k miles before the tranny gave up the ghost. I don't know how the previous owner drove it. I see many people with supercharged Raptors with stock 6r80 and tons of miles. I most likely will not have this truck another 100k miles, so I'm not sure it makes sense for me to spend the $$ on a built transmission if another stock one will give me at least 80-100k miles? I don't off road, drag race, or contantly smash the throttle all over the place. I enjoy knowing its there, and every now and then romping on the interstate passing someone etc.
Anyone ever pull their transmission on their back? I don't have a lift. I'm mechanically inclined, but not sure how bad this would be without a lift. I've been quoted ~1k to pull and replace. To be honest I think that may be worth not having to deal with it.