Also need to check perpendicularity to faces. The offset dowel only helps “center” the shaft. When we were racing 4spd cars, there were several Lakewood blowproof aftermarket bell housings that we needed to have faces remachined. Off the top of my head, up to .003” was max.
When sweeping faces, you must figure indicator sag or you could make a good part a problem. (Adding— if checking in a horizontal position, vertical measurement most likely “not required”.)
Without actually verifying what you have and assuming there is no bind and the new pressure plate is working correctly, I would still try a floor stop at just a smidge below “free engagement” needed. Not costly, and would help point in next path forward if failed results.