Now I realise this is 100% on me, for looking at these air filters and going, meh, they'll be fine:
Because a you can see, I finally made new ones and I'm calling it misfire fixed! You can go full throttle and it just goes. Great success!
So now I've got a new problem (of course). I think it's fuel starvation. Prolonged full throttle runs, 80+mph, really giving her all the way, it just dies after a short while. It just loses power, which I can tell you, is quite unsettling when thinking about all the money, time and effort that could be self destructing. It regains power after backing off and rides normally.
This all screams fuel starvation to me, but weirdly it never did this before. I haven't checked the fuel tap strainer yet, but I will. The question is, does the XS650 need two fuel taps? Mine had two, but after multiple rebuilds, cleaning and polishing (they're the dreaded vacuum operated ones) I could only get one to work reliably. I blanked off the tank where one was, and I teed off the delivery so it feeds both carbies, and the balance pipe between the carbies is still there too.
I would be surprised if one tap couldn't deliver enough fuel, but it came with two and I suppose Yamaha didn't do that just for fun? If two are needed, I'll ditch the vacuum ones and fit normal types.