Im just talking out loud here:

90-93 integra halfshafts are DIFFERENT than 94-01 Half shafts

One has a male end, one is female

Auto Halfshafts are different than MANUAL halfshafts

Axle seals are different between CABLE and HYDRO Transmissions

Now, if you used an AUTO BLOCK, wouldnt you have to use the AUTO Halfshaft? Since the halfshaft bolts to the block, if the motor was originally an auto, the manual shft wouldnt fit correct?

What you need to do is take a picture of that halfshaft you HAVE and where its not bolting up so we can see it.