the reason that you can't use the tranny is beacuse of the ATTS system it uses a tq converter that allows it to work like a LSD. So with the tranny mounted to the and the ATTS system installed the halfshaft and axle don't work.

Go to slhonda.com and search 98 prelude sh 5 spd and you will see the tranny and the ATTS system and it should make more sense

Also there is no such thing as an OBD1 96 P13

92-95 P13 = OBD1
96 P13= OBD2
97-01 P5P= OBD2 Immbolizer