The safety switch system by and large works by providing alternate earths.
One of the few really good ideas universally taken up.
First try disconnecting the clutch the nest time it plays up.
If the problem goes away check the clutch itself for a short.
If it does not go away then you have a safety switch fault, a wire that is shorting out or even an internal problem in the PTO switch.
These are a PIA to find and generally the system used is to replace with a known good one till the problem goes away.
Or in your case to bypass each switch one at a time till the problem goes away.
Weather you are up to this depends upon how well you understand circuitry and if you can read a circuit diagram.