A small update. It is sort of fixed now.
(After typing all of this I realised it is not really a small update. Also it's probably very boring if you are not me. The important bit is that it's sort of fixed)
The trouble I've been having is that the Honda dealerships only want to use genuine parts. Since the 650 was never sold in Japan there are no spares on the Honda part systems (the VIN doesn't even come up). They all want to get them sent over from Italy. I was told it would take 4 weeks for a new set of spokes. So that option is out.
Independent dealers seem to be quite happy to do the work for a fairly large sum of money, but they want me to supply the parts. I can have them sent over from the UK but when working out the time and money it doesn't end up being any better than the main dealers.
I did find a place that would source a new rim and set of spokes locally for a sort of reasonable price, but the lead time was so huge (5 weeks + 1 week for assembly) I just can't consider it.
But after spending 4 hours at the garage working all of that out they called some other guy to come and look at the wheel and see what he could do. I should say that the wheel isn't seriously damaged, but it is definitely out of shape. This guy spends a long time complaining that the spokes are so badly corroded that they will break if anyone even thinks of taking a spoke wrench to them. So he them pulls out a spoke wrench and adjusts them anyway. And he did a good job. The wheel is now significantly more round than it was this morning.
The problem hasn't been fixed, it has just been offset. Now that the wheel no longer feels in danger of collapsing I shall probably just carry on. I have another 3 weeks or so in Japan so will only worry about it if it gets any worse in that time. Otherwise it can wait until I reach KL where I know I have the time and means to sort it properly.
Thanks for all the help and suggestions from everyone. It was very much appreciated. There seems to be a really good community here in Japan.