It should bolt up just fine, if anything with the C4 the yoke will stick in less then a T5 or Tremec. We use the Ford Racing pretty much universal on a Fox Body with any of the manuals, AOD, AODE or C4
I just did a c-4 swap in my 94 gt...THE fms SHAFT WAS TOO SHORT///iirc IT WAS 1-1.5" TOO SHORT. I bought a custom one from Strange, but I also used their 8.8 yoke, and 1.350 u joints.