You're not that far off. Normally, in most cases, a problem like that turns out to be a loose ribbon cable; one that wasn't securely connected to begin with or excessive heat worked it loose. But still, re-seating the connections should fix the problem. As far as the ATI chip on the daughter card, I think that may be a chipset; probably an early form of Northbridge, since it's physically connected to the RAM and CPU. The so-called Southbridge would be a second chipset on the logic board, probably located directly underneath the daughter card, so that the 2 chips take advantage of the short bus connections to and fro.
Just yesterday I had to tear mine apart to install the replacement hinges in the LCD display, but didn't have enough time to verify what I had in my Pismo. I haven't experienced the same problems you've been having, but there have been some fluke moments in the past, where I couldn't get any response from the USB. Restarting the Pismo did solve the problem. It might have been from excessive heat during normal use, but that only happens if I am running Firefox and/or watching Youtube videos.
73s de Phreakout.