Well the problem wasn't strictly a ground loop issue, let's just call it "user error" and move on, shall we?
So once the previous problem was sorted, I hooked up a LED to the knock filter output, and with the engine off I tapped various spots on the engine with a spanner but got absolutely no response.
Resisting the urge to whack it harder, I re-checked my wiring and noticed I hadn't plugged the knock sensor back in
Once that was done, sure enough the LED flashed differently depending on where (and not how hard) I tapped.
I started up the engine, and the LED went mad so I backed the knock filter settings right off until it stopped.
With the engine idling, I increased the timing by 10* and immediately the LED started flickering away. When I set it back, the LED stayed off.
I think I'll get a cleaner signal when I move the sensor away from the injector/valve, but it looks quite usable as it is now.