G'Day Tim, you're right about the disc to fork leg clearance, on the bike I'm building for a customer, the clearance is approx 5mm on the left (shifter) side, and 10mm on the right (points cover) side.
You need to make some spacers between the caliper bracket and the right fork leg so that the hinged caliper arm runs parallel to the disc, or else the pad won't sit flush, and will wear at an angle.
You can do it with washers, mine came from Rex Wolfendon (TRex Racing) many years ago, and he'd made up some little alloy spacers and welded them to the bracket. Good idea about stripping that engine if there's a lot of silicone present, and it won't hurt to freshen up the engine with new gaskets etc, while you're at it. Cheers, Terry.