I would tend to agree. This is one of the oddest issues I've seen in some time. And it seems you are indeed alone on this for the most part. I spent some time searching and about all I came across was your threads on mulitple Droid forums.
I have been racking my brain on this one and I am coming up with nothing. It almost seems like you received the wrong display for this device or something yet it works with stock. Hboot and radio up to date and even if they weren't, what the Hell would they have to do with touch screen functionality?
I mean it's almost like you have some top secret experimental device here that they sent out by accident. And what are you gonna do..."hey can I get a replacement phone cuz when I root and load any custom rom, my screen breaks?"
There's just one crazy idea you might try, it's the only thing I can think of. Try a different SD card in the phone. It's the only thing that makes even the slightest sliver of sense to change outside of a new phone or getting incredibly lucky and finding a particular kernel that works and if you do find one, I'd call it a shear accident because to my knowledge, nobody is deving for this issue b/c nobody else has it.
I'm still thinking but my brain hurts.