Here's what you're dealing with on the IIfx:
Pin 1 on the ADB connector is data. There is an inductor involved (UB15) and maybe if that's damaged, or even if it's not, maybe that's acting like an antenna somehow? Just speculation... I have a Ham radio license but I'm still not great at that stuff. Or there could just be a weak short inside the UB15 component between the data line and another ADB supply line. I don't quite follow that schematic symbol. It's some type of quad-inductor?
There's also a 470 pF capacitor connected to the data line: C60. I would definitely check that one. Make sure it's actually connected to ADB connector pin 1.
Make sure there is a high amount of resistance between pin 1 on the ADB connectors and each of the other pins, especially pin 3.
Q1 at location 1A is used to pull the data line low, when the Mac is sending ADB commands. If it were damaged, you'd have trouble with ADB communication but I don't think it would cause glitching like you're seeing.
<speculation>Your symptoms might be explained by a weak short between ADB data and ADB +5V on the ADB connector side of those UB15 inductors. This might not cause a huge problem when the Mac is sending data, because the short to +5V is on the other side of the inductor from the Q1 transistor that's trying to pull low. But when devices tried to send data, it would be a more serious problem, C62 would be partially discharged and a surge of current would need to flow through those inductors to replenish it even after the data bit ended.</speculation>
If you still can't find the cause, I would start replacing all the components in the red box one by one.
When you see voltage bouncing on other signals during ADB transmissions, does it happen during the whole transmission (command and response), or only during the response part? See here for a diagram:
https://www.bigmessowires.com/2016/03/30/understanding-the-adb-service-request-signal/ Everything from the beginning up to the stop bit comes from the Mac host, and everything after that (if there is anything) is from the answering device.