I've pulled and replaced my engine more times than I can count....And every time, I've pulled and re-installed the TC. To re-install the TC, simply push it onto the input shaft until it won't go anymore. This is the FIRST stop...Turn the TC clockwise until it can be pushed on to the input shaft further. (this is the second stop) Then, turn the TC clockwise again until it can be pushed onto the input shaft even further. This is the THIRD (and final) stop. Take a straightedge (like a 3 ft level) and hold it across the transmission bellhousing face. The TC studs (if equipt with them....if not, then you should put them on at this point) should NOT be able to touch the straight edge. When you put the engine back in the car, the TC should NOT be touching the flex plate upon initial installation. In fact, even after the engine and the trans are bolted together, the TC should not be touching the flexplate. There should be about 3/16 of an inch space. When you put the nuts onto the studs, this will pull the TC back out that 3/16". This will have it correctly put in the trans. If the TC IS touching the flexplate prematurely(i.e. the TC can't be pulled to the flexplate), the TC is not seated properly and you will break the pump upon start-up.

Hope this helps..