I feel like we might be missing something easy. Larry Pina wrote a bunch of books that had helpful sections of the form, "If X is wrong with your Mac, replace Z or resolder Y". I don't think he ever did a book for a Mac as late as the Q700, but since it isn't using Egret/CUDA yet and still has distinct VIA 1 and VIA 2 chips, I think its ADB subsystem might be analogous to the older machines.
I know there was/is a PDF version of "The Dead Mac Scrolls" kicking around, but I can't remember if it covers the SE (earliest? machine with ADB bus). He also had a series of books of the form "[ ] Repair and Upgrade Secrets", where the first one was Macintosh, but there were later books for the SE/30 and I think for the Mac II.
I would check one or more of those, the ones that applied to ADB Macs, for the symptom you're having.
You might also take a look at "The Guide to the Macintosh Family Hardware" or perhaps, the appropriate chapter of "Inside Macintosh" and see if there's something fundamentally different in how the ADB bus handles keyboard input vs. mouse input. The symptoms of your problem are very strange and I feel like it should be pointing us right at something, but my knowledge of these systems was never great, and my memories are old and leaky.