I don't know if it makes a difference whether you get the master/booster from an auto or manual truck.

Your calipers are already the same type as used in the Gen I V6 trucks. You can stick with that, if you like, but you'd need the Gen I V6 rotors, caliper brackets, and dust shields.

For any Gen II brake upgrades, search the board. I haven't done any research on it yet, so I don't know the details, but I know others have. I believe all that's needed is calipers and caliper-brackets, and some minor brake-line modification, but I don't know for sure. Here's a starting point:

http://www.4x4wire.com/forums/showflat.php?Cat=&Board=UBB69&Number=1013083

EDIT: My brakes are fine now as they are, since I can lock up 33x12.5 M/Ts on dry pavement. I'm only contemplating upgrading from what I currently have if I move up to 35s.

Since your's is an 88 as well, it has the 4-banger engine as well. I wouldn't move up to anything more than 33s unless you've upgraded the front axles and front diff to the V6 axles and diff and swapped your diff gearing to 5.29s (both of which I've done).

Yes, you could put in a bigger engine, but your front axles and diff likely would come apart if you had 35s. Heck, you might break a rear axle also. That's why I'm staying with the 4-banger. It drives fine on the highway with the gearing I have, and it has plenty of torque on the trail, but it's not so much power that it hammers my drive-train to pieces.