Just an update -
If you have EKF3 on, turn it off.
My backend_logging is "file only"
I had bumped my log_buffer up to 40 and it was causing problems(EKF 3 errors out with insufficient memory at 40) - changed to 20.
log_bitmask to 45054
log_replay changed to 1
This has cleared up my issues, I've been connected via USB only for an hour now - and have had Telem the whole time with fast updates.
I was also able to reinstall my Edison, and actually power and connect the PH2.1 via usb.
I think a combination large EKF3 overhead, and large logging had simply overloaded the FC / Edison, and the combination was keeping the unit from booting on USB. Of course, I'm sure there's way more to it - nonetheless, it's working.
I'm going to post my setup experience here in a minute - now that I think I've worked much of it out. If for nothing else, to help somebody whom might be having issues.
Edit - while Craft & Theory may need to change some code or buffering or something for new EKF3 messages, I really don't feel like it's entirely their issue.