Thinking out loud and with all of your input, I think it must be the pilot bearing. It was new when I did the swap.
After I replaced my throwout bearing I put a little grease on the end of the transmission shaft. I believe it quieted down the pilot but the noise is coming back.
The tranny is coming back out
I'm not sure what I did to damage it? I used a heavy duty one but not sure of the name. I had to damage it on the install.
Hey did I mention the car rip's!!! It's a LQ9 I bought from Jody with his mods, heads, cam, etc. I put it into my 69 firebird. Fun as heck to drive and it just rip's!!1