If the 93 is a CCLB E4OD and the 88 is a SCLB ZF5 how can I do the trans swap? What is the difference in driveshaft lengths? The junkyard has very slim pickings
Are they 4x4 or 2 wheel drive?
If they're 4x4, measure the two transmissions from the bellhousing-to-block bolts to the transfer case mounting flange. If they're the same, you won't need to do any driveshaft work...just keep the transfer case that's on the truck (it'll bolt to either transmission) and you should be good to go
If they're 2 wheel drive, the same applies with the transmission lengths, but the trans output shaft yokes may be different sizes, so you may have to use a special U-joint. IIRC they exist on the shelf, so it's just a matter of sourcing one.
There's an expansion joint in the driveshaft that can take up SOME of the slack, but IIRC it can't take much...maybe an inch, but I'm not 100% certain on the exact number. Any more than that, and you're going to have to resize driveshafts.
If one's a 2 wheel drive and the other's a 4x4, you have a problem. Converting a 2WD transmission to accept a married transfer case is not practical; ditto vice-versa If the '93 is a 2 wheel drive and the '88's a 4x4, you could leave the transfer case bolted to the transmission and either use it as a 2LOW setting, or leave it in 2H and not install shift linkage at all. If the '93 is a 4x4 and the '88 is a 2 wheel drive, you're either going to need to find a 2WD ZF or get a divorced transfer case, and do custom driveshaft work. Not insurmountable, but not simple, either.
As noted before, the '87-'91 and '92-'97 pedal assemblies are different enough that you're going to need to find a manual transmission pedal assembly from a '92-'97 truck. They were still available from Ford a couple of years ago, but they may have since been discontinued. The good news is, everything else (clutch hydraulics, floor pan insert, etc) should swap right over...