I just found this guide which hadn't been finished, I haven't gone through it too thoroughly so if you see anything wrong/worth adding then comment and I'll put it in....
I can safely say, having done both, it is MUCH easier to pull the engine when doing a box swap unless you have a nice hydraulic lift!
The things you will need to convert your auto Supra to a manual are:
1. An R154 manual gearbox (You can do W58 too from an NA but this is based around a turbo box being fitted)
2. A flywheel (and 6 bolts)
3. The lower mounting brackets that attach the bell housing to the engine
4. The master and slave clyinders + pipework
5. Smaller brake pedal from a manual car and the clutch pedal
6. Front section of the prop shaft from a manual car
7. The cover plate between the engine and 'box
8. A clutch (friction disc, pressure plate, bolts, fork and release bearing)
9. A pilot/spigot bearing (the manual cars have a bearing on the end of the crank, autos don't have this)
You should get new clutch and flywheel bolts really
All the holes are pre-drilled so you don't have any major work in that regard, it is all just bolt on. You can easily do this in a weekend or if you're quick in a day.