It is a B series transmission. Yes, it will fit.
both transmissions came from 89-93 models of teg and civic models and both cable types. b16 transmissions are interchangable and should not encounter any problems when swapped. try to check the way you put the axle.. i experienced the same problem but in my case the axles seem to be longer. what happened was the axle bearings were put upside down. (i have the bearing with the sqaure housing at the bottom part of it)