Did the brakes work ok before doing the swap? You didn't mention it, so I presume they were fine. Otherwise, I would suggest checking for leaks, bench bleeding the mc, or replacing it.
So here's my suggestion presuming everything was fine before.
I have heard both ways. Some say the 87-93 mc works ok and others say the bigger calipers require more fluid movement. I would guess the truth is somewhere in between, and the difference you're experiencing is partially due to an out-of-adjustment rod. You can try adjusting it (or measuring it, although I didn't have much luck trying to do that with the amount of precision required.) My rod was adjusted too long with the cobra mc and booster (sn95 brakes). They worked perfectly for about the first 15 minutes of driving... then the front brakes would start dragging/sticking. Adjusting the rod is pretty easy, so you might try it. Remove front drivers side tire. Remove both nuts holding the proportioning valve in place (in the inner fender area). Remove both nuts holding mc to booster. Pull out on the proportioning valve till studs are clear, then pull mc out far enough to access the pushrod.
You will see the adjustment nut on the tip of the rod. You'll need a small pair pliers/vice grips to hold the rod and a small wrench to turn the nut.
