You're not gonna see a Japanese-designed 4-stroke twin with a 360* firing order. The XS650 motor is descended from the 500cc. twin designed by Horex in the 1950's; Horex went bust, company got sold to the Japanese, and two defunct Japanese companies later, Yamaha wound up with the plans. When a big (for the day) 4-stroke motor was needed in a hurry, Yamaha knocked the dust off the Horex plans and rushed a 360* 650cc. twin into production.
Meanwhile Yamaha's engineering department got busy designing their own motors, represented by the XS360/400, XS500, and TX750--all 180* twins in the Japanese tradition, and considerably more sophisticated in design than the old 650, which turned out to be the most popular machine of the whole bunch!
I hope that a walk through the manuals makes it very clear that you cannot "convert" a XS500 to a XS650 and that if you could, it would be a mistake. The only item you need to be cautious about in the 500 motor is the cam chain adjuster. It's automatic, and prone to failure if not changed out on schedule.
5twins, I can't agree with your assessment of the 500 as crusher feed! Yeah, parts are hard to find--so much the better, that difficulty is just moron repellant. The motor is very lively, and a good one will leave the XS650 eating dust. Handling is nice too. Clean specimens are getting very hard to find.