New developments, I had a mate take a look at the GSX last night and he checked my timing(was spot on)
And the cams, spot on again.
He spotted that once the alternator was torqued on to the shaft, that because I had removed so much metal by lapping the tapered shaft, it now was forcing the starter drive gear into the engine casing!!!!!!
So the only solution is to remove 1.2 mm from the drive gear so it will all fit up nicely and not snag.
It explains a Hell of a lot that I couldn't figure out on my own and I would never have discovered without help.
More info once I find an auto shop to lathe off the 1.2mm.