Unless the clutch is pretty darn new, now's the time to replace it. Even if re-using the old clutch, you'll need a clutch friction plate alignment tool (or an old tranny input shaft) to hold the friction plate centered while tightening down the pressure plate.
The front square mounts do fit all years - they replace the old hockey puck style which are discontinued. Supposedly they are an improvement. I would recommend new rear mounting bolts, washers, castle nuts and cushions ("insulators" in Toyota parts jargon). It's probably too late to bring them in from the dealer though.
Having done it both ways, I highly recommend bolting the engine, tranny and t-case all together and then drop it in as a unit. Stabbing the tranny while the engine is in is easier when it's all out on the floor. It is a true PITA doing it while the engine is in.
Hint on the tranny shifter install: the retainer goes in CCW to lock it in, CW to get it out.
Another hint, when dropping the engine/tranny/t-case in, go ahead and put the alternator and water pump on in advance, it'll help counterbalance all that weight at the rear. Doing it that way, it also helps to have a load leveler for the cherry picker, and a couple of long pry bars (I use 6' sections of 1" pipe) to maneuver it in and onto the mounts.
I'll try to see if I can make it down tomorrow. In the mean time, here's some photos and narrative to help:
http://risingsun4x4club.org/forum2/showthread.php?t=1629&page=5
That starts at page 5 of 14
