i put a 90 lx trans in my buddies 94. as you already said, you need the 88 bell as well as the 88 clutch fork.
we put a 94 fork in it but had to grind the bell out for it to fit and then grind a small corner off the end so it wouldnt hit the car body under heavy acceleration. (trial and error)
as far as the shifter went, it fit right in. 5/8ths wasnt even noticable. it was already a 5spd car so dont know about the floor for sure for you.
the cross member went without modding, the holes were slotted so it allowed the trans forward no problem. once again this was an already 5spd car/crossmember.
the drive shaft could use a 5/8ths spacer too to get full bite on the splines although we did not and never had a problem. it just hangs out farther.
is the aode shaft the same lenght as the 5spd anyways?
so if you didnt know, which i think you said you did, the basic problem is the pre 94s were 5/8ths shorter in the input shaft and bell. the clutch fork also comes in the bell at a different rotation (closer to the body of the car) but not a prob.