yeah, but you can use the flywheel from your current engine, no biggie, but if it's worn, get a remanufacturered or new unit from an auto parts store...
all 2.3's are the same, all trannies will bolt up to all engines, but the early ranger trannies won't hold up to the power for very long, the M5OD is an exception and works fine. my tranny had around 200K on it before I swapped in the turbo engine, went to play in the sand with some friends, gave him a ride and he said he'd never seen a tranny shifted that fast (it's worn in now), and he's a tranny and axle tech... sure it grinds a bit when I do that (I don't shift like that all the time) but with his help I can rebuild it for a few hundred bucks... (according to him it can be done in about a six pack of brew)
with an '88 you should have an M5OD so you shouldn't have to worry