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After having bought the new mains from the Yamaha dealer in Dublin, I found that was about as far as they were going to be of any help. I then got in touch with Tony Hall of Halco Tuning in Salisbury, UK. His knowledge of the XS650 has to be the best around, and he was able to supply all the parts I needed albeit at a price! On one occasion I'd ordered parts on the worst day of the Euro-Pound exchange rate, and got a hell of a fright when the credit card bill came! 
The engine had been stripped fairly recently, but had been rebuilt using a 'liberal' amount of Instant gasket - the oil way to the gearbox was full of the stuff. I cleaned all the oilways using the pressure washer and degreaser.  New rings, oil pump innards, oil filters, oil seals, starter bendix and other sundry bits went into the engine. The cases were cleaned using oven cleaner and a pressure washer, the oven cleaner (caustic soda - use rubber gloves and eye protection) did a great job as long as it was only left on for about ten minutes! Otherwise I  reckon the cases would have begun to disolve... 
The clutch cover and alternator cover were polished using a cotton mop, and came up not too bad, but I've yet to discover a way of keeping them nice.  I gave the barrels a 'good hone' and painted them with black exhaust paint. 
The engine stand in the photo was a great asset in rebuilding the lump, and all went back OK. I used a novel way of getting the pistons in the bores, placing the pistons in before connecting to the conrods - not a method I'll use again!