(Bob-not really in reply to your post, just an addition to the thread).
I don't think that the yanmar is exactly an orphaned tractor. I imagine Len Sheaffer could get you almost any part you need for the machine, especially since it is a US model. There may be some parts that are unavailable, but once a tractor hits about 10-15 years old, even JD/NH/Kubota parts support may begin to deteriorate. I had an old JD 2010 (1964 model) and only a few parts were available from JD - or course, that's almost 40 years versus 10/15 years. I would also say I found every part I was looking for either from aftermarket dealers or junkyards, though.
The grey market tractors seem to absorb an undue amount of criticism. I have had a Yanmar F16D for over five years, over 500 hours of operation (primarily mowing/bushhoggin/postholedigging/spraying), and I've replaced the filters and fluids for maintenance and charged the battery up a couple of times - that's it. I have no idea if I will have parts difficulty - but I'm gonna have to need parts first.
For your case, though, I would probably lean to the JD, simply because it already has a loader. A loader for the Yanmar will probably go $2,000-$3,000, although the Yanmar comes with quite an assortment of 3PH items. Depending on how many of those items you actually need and will use and would have to buy for the JD versus the cost of a loader for the Yanmar would be what I would use as the final judge of which tractor. I'm not that familiar with the JD 650, but I think that the tractors are of similar size aren't they? If you need all the implements and can add a loader for less than the price of the JD and the implements you would buy to use, then I would go Yanmar....if not, JD.
I doubt the above babbling really helped, but good luck to you.