[Christ]

2.8/3.1 transmissions bolt up, so that covers the flywheel/clutch/bell housing issues. The axles are pretty much the same diameter/spline count that I know of between just about all the 60* V6 engines, but even those aren't hard to source, if they're different. Often, transmission mounts are a matter of sourcing some plate steel (2 or 3mm) and welding it up, which is probably within your means if you're taking on the project anyway.

The pedals are only a matter of cutting one edge off the auto's brake pedal, then mounting a race pedal from Summit or similar, with the corresponding clutch actuation type for your trans (fluid or cable). Shift linkages are a matter of following the basic installation that you pulled it from. It will, in most cases, follow the same routing. Mounting is the same deal.

The interface problems are the hardest part to solve, provided that you dont' have a separate transmission controller. IF you do, you're set on that as well, by simply removing the TCU in most cases. You'll probably run non-optimally, but you can also reflash most ECU's to whatever specs you want anyway.

At least every one I've done has ended up that way... I'm sure someone can come up with an exception.