Just had a closer look at the engine... it was covered in metal shavings from all the welding and grinding I have done on the frame (don't worry, all the apertures were plugged and taped shut). In itself no biggie, but the bike has sat in a very damp environment for months and the shavings started to coagulate and rust. Not good! I washed the engine today and although there are a few spots where the rust has coloured the (baked!) paint, the damage is not too great.
Lesson learnt: Rusty items WILL discolour even the hardest paint.
Still awaiting the local bike shop taking the swing arm bearings out... (I could not do that myself). Then the frame and all the bits are off to the powder coater.
Received my new Benelli front wheel (which is perfect!) and Jay from KZriders will be making me a new VIN sticker