I think you may find it faster and cheaper to get a known good engine from a reliable source (one of the guys on here Geoff33 perhaps) and replace the whole unit. keep your engine for spares and you can strip it down in your own time and get an understanding of how they go together.
Thunderaces' figures are pretty good, so if you pay £150 labour + £30 - £50 for the gearbox, plus another £30 - 50 for oil, filter and gaskets, then you have to get the engine out of the bike and back in! soon adds up, get a good engine for £250 and have a nearly complete engine for spares. Happy days again

That thought crossed my mind but it's find a known good one that's the problem, and getting it in the frame! I think I'll just have to deal with no 3rd gear for a long time