No mikuni guru but you can still get kits for them, given all the issues you have found and conquered so far I'd be inclined to strip it, sounds like the petcock is suss as well, while your at it :)
Agreed on the base gasket. Easy job.
Anyone got a trick for removing the rear cylinder with taking the engine out? Its just like janga in the frame
Bugger. Did you make sure the base gaskets were on correct and not covering the oil return hole?