I have recently fitted Megsquirt to my Herald, so ignition only but about to start on the fuel side.
I made up a bracket to hold the sensor and bolted this to the timing chain cover, it does give you some flexibility. I mounted mine about 50 BTDC, you can correct for the position of the sensor in the software. I think the manual recommends mounting it some way BTDC as there pulse train will before reliable before the fitting stroke.
I would not take the timing pointer off as you will need to check and calibrate the timing (with a strobe) and you need the timing parks to do this.
Am surprised that the trigger wheel will interfere with the pointer, on mine (its a 4 cylinder engine) the trigger wheel is slightly smaller diameter than the pulley, Will see if I have a picture that I can upload.