I ruined a torque converter once by bolting it up improperly. It made a raspy scraping sound when I tried to turn the engine over (and when I started it!). I, too, thought it was rubbing the separator plate, but it was not. If you can't find any scratches on the plate, and your flexplate seems to be fine, your bellhousing is fine, make sure you check out your converter.
Aside from the bellhousing itself breaking, which will be loud and obvious when it cracks, you might notice some damage to the pump if you get it as spectacularly wrong as I did. Just check for hairline fractures around where the input shaft of the transmission is. They will show right up, with a dab of transmission fluid, if things are clean.
When mating the engine and transmission, if you've got everything seated right, it goes together *easy*. No fuss. If it's not perfect, don't try to get that last 1/4" with the bolts, because I promise you, it's not "right". I found out the hard way, as many others have. =)
EXTREMELY important point, unless one enjoys re-doing with $$$ and time. I found if room allows it, (sometimes tilt engine backwards to clear junk above with trans
, use two threaded studs, long enough to have unthreaded shank, maybe 3 inches long. Bolts can be used; cut the heads off, file smooth. Use them in two places best near top of bell, but not too close together, slide trans
forward with bolts holding it up in front, jack under pan, seam between eng/trans
nice and even get to the dowels, which should have been cleaned and greased, holes in bell as well, that baby should slide home using your hands.