You said in the bellhousing area there is a ticking/scraping type of noise & that you had trouble getting the tranny to seat. I can't speak to the ticking noise but I have a possibility for the "scraping" noise.
I once had a dealer install an upgraded clutch in my 85 GT. When they did the install, they somehow managed to slightly bend the aluminum block plate that the bellhousing seats against. The block plate was bent just enough that it rubbed against the engine side of the flywheel thus causing a scraping sound. In my case it did not cause any problems with the tranny not easily seating properly.
Since you had trouble getting your trans to seat properly though, it's probably a good idea to check the blockplate to ensure it is not bent, the ck to see that it easily fully seats against the block, and to ensure the counter bores where the trans front bearing cup, and the starter stick the block plate do not have burrs or some other issue causing binding.
Hope this helps and that you don't have any problems with your engine rebuild.
Ed