you say you swapped the tranny, but didn't say why or what trans you used--any chance what ever you are using for a pilot bearing could be a little too tight on the trans input shaft now (ie, making the input shaft spin even if the clutch is disengaged), or the shaft was burred a little and is stuck to the pilot brg now that has been pulled in by the bolts?
just another thought if the hydraulics aren't an issue and clutch is found to be installed correctly
