I made the swap a couple of years ago. I kept my 3 speed tcase and used the adaptor gear for the different splines and the two spacers to line everything up correctly. Lessons learned, moving the crossmember back is huge. You keep the parking brake and its accessible. I bought 4 speed drive shafts off of craigslist and correct pinion flanges from cruiser outfitters. But the front drive shaft ended up being too long. So I had a new custom drive shaft made for around $150. I also have a desmogged 2f that I believe is out of a mid 80's fj60. The po kept the original 3 speed transmission and clutch setup accept the push rod for the clutch fork is this crazy non return spring setup that Toyota tried in the 80's. Kind of a pain. I am gonna switch the clutch fork out this spring, just so I have the correct clutch fork and push rod. And I purchased a tcase saver off of mud Also this is the best time to replace seals. Especially the rear main and tranny/tcase. Here's the link to my swap. If you have any questions feel free to ask.
http://www.risingsun4x4club.org/forum2/showthread.php?t=19023#
http://www.risingsun4x4club.org/forum2/showthread.php?t=19023#