Oh nice. I am going to out Lord of the Lake on the Sunday for a look so ill keep an eye out for you. I'll be on a Red/White 2J MC18 so if you see me, sing out.
Something else to check if your bike is a hybrid (like mine)... I believe the flywheels are a different size on the PGM1 bikes vs PGM2 bikes. It might be worth doing some research on what the differences are and if you are running the correct one as that may well affect your timing too. It does sound a lot like a carby issue though as you mentioned.
Have you got an air compressor to blow out the galleries in your carbs.
My 2J runs a PGM2 too so worst case I may be able to help you troubleshoot by substituting some parts (carbs/pgm etc). I have a bunch of spare coils etc too we can try potentially.
I'll PM you my number and let me know what you want to do. Woo, teamwork!
Cheers,
Andrew.