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You'll have to swap over the manual pedal assy., drill the firewall for the hyd. clutch master cyl. It's stamped where you need to drill, I recently did it's pretty much the same swap when I dropped my 82 cab on my 86 chassis(coincidentally, it was a F250HD 4x4 ex. cab also), even though they were both standard, I had to swap the entire pedal assy, which was the hardest part of teh job, even though I shortened the chassis 22" and put a regular cab on...
For the shifter, the floor is stamped where the plate sits in a manual, your best bet is to take the plate out of the manual cap, sit it in place in the auto one, mark and drill the boltholes, and, then cut the opening about ¼" inside of them(that's about where the factory did it.)
As for your computer issue(from your other post) that wiring just unplugs, and you can plug in your standard DS-II wiring.
Evan
86 F250 HD XLT Lariat Explorer 4x4 ex. Extended Cab: 8800LB GVWR 460/Edelbrock 1411
T19/BW 1345/3.55 geared Full Floater 10.25/Dana 50 TTB
265/75R16's on Whitespokes
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