Recently had an engine swap done (cam belt snapped, the joy) since its been done I have had an issue with the radio, the issue being that whilst the engine is running the bluetooth, auxillary and usb do not function properly (they turn on and off intermittently) so I cannot connect anything to the radio. After pulling the fuse and resetting the radio I was able to connect via bluetooth again whilst the engine was off. Would swapping to a new fuse solve the issue or is it a deeper routed problem with the radio.

The first thing that comes to mind is you might have a lot of interference and possibly voltage spikes on the 12V supply. As the engine's been swapped this suggests maybe one or more earth connections have not been made correctly so checking them would be my first port of call.

Any recommendations on where these connections could be (assuming all located in engine bay)?

Sorry, I can't help with that I'm afraid. I no longer have my Mk3 and I can't find any information in Haynes. Hopefully one of the true experts will be along soon.

So I have found the "common" ground points next to the battery and under the air filter. I have only one ground connection under the air filter though, everything I have read and seen suggests there should be 2, I have had a look and followed as many cables as I could find and could not find another. Both points have been sanded and protected after reconnecting the cables/screws. The radio is still showing the same issue. Works fine off pure battery power but when the engine is started no USB, bluetooth or aux. Wondering if there is still something I am missing or a potential alternator issue.

I want to avoid taking it to Ford because A: I imagine they are likely to suggest a new unit/bluetooth adapter (most likely would work from my research. And B: Wouldn't have the parts to fix it