Are you using any sort of VGA adapter? I had a problem with a 2000 that just simply would not boot (couldn't even get to early startup) if I had a VGA monitor connected. Something to do with genlock circuitry, I think. It was a straight-through pin-conversion adapter, not one of the silverboxes which has some added logic.
The other thing I can think of is that the Amiga is getting confused by a hidden RDB flag. I had a 4000D that would also refuse to boot after I connected a new hard drive. I eventually found some combination of drives that allowed me to boot. I was able to get into HDToolbox and received the "drives have been added or removed from the system" message. Acknowledging that message and saving changes sets the RDB flag that there are no more drives and that the system should stop looking and start booting.
If you connect the 4000T's drive to another Amiga, you might be able to set that flag manually (with a different hard drive utility - just make sure to back up the RDB first!) and get the machine to boot.
