88 = 21 splines on the imput shaft
89-91 = 20 splines on the imput shaft
Most 88-91 Civic/CRX trannies say L3 on them so its sort of hard to know what exactly the tranny is due to lack of any info we know to look up the number and see what it was.
As for clutches I have an 88 ZC Tranny and I used a 88 CRX Si clutch and it worked fine.