i just stumbled on this thread,
JTAG is something that's been done to many phones, qualcomm is popular in that aspect.
I haven't read the whole thread just glanced,
have you tried looking at the service manual?
its posted here at modaco.
Before you try anything, try clearing the eprom, i haven't opened my omnia, nor do i intend too, but if you just disconnect all power sources and then reset it, and then powering on, it has a chance that it will work, because a file or executable might be stuck in the eprom and preventing it from starting.
I'll catch up on what you've done so sorry if this has all been done.
All the best