toneless wrote:Gap should be the same on both lobes.

No1. is the LH cylinder.

Thanks for your reply and apologies for not responding sooner, I do appreciate your input. I've removed the gens (again) and checked all measurements and they are identical apart from a lug on the body of the lower (rh) one. I was hoping the suspect one was broken off but it doesn't appear damaged at all, and as both units magnet projections are the same I'm very confused.
I've now set the bike up to run and will test voltage readings from the gens to the pgm and from the pgm to the coils & plugs. I'm hoping the problem will appear and be apparent.

I will advise and thanks again.