After some wrangling I got the airbox and plenum mounted.
I spent an hour looking for my hydraulic jack as I was going to remove the engine mount (save one) to make some more space. Never found it, WTH. I figured I would get to work, then look again. I thought I might be able to get away with it without removing the carbs, but not a chance. And then I remember how easy it was to remove carbs with pods, so no big deal. Mounted the airbox and plenum and left them unbolted to the frame, slid the carbs back in, and everything lined up nicely. Had the exhaust off as well, so put in the new seals and cleaned up the chrome behind the silencer. While I ad the tank off, I replaced that one last damn allen bolt on the valve cover and had a look at the tach drive. It's in one piece thankfully so I imagine it is just the seal -- will pick one up next time I am in the USA. Frustratingly found two imperial bolts at the motor mount in the front -- those will be replaced too.
Hooked up all the hoses (am missing the hose for the plenum but I have one on order) and tightened and double checked all the motor mounts, the exhaust and the RHS foot peg. Fired her up and she purred.

Went out for a ride and there is some improvement -- it idled smoothly just after 1k (it was idling around 1.2k before, with a little chugging. It was a lot quieter. But...
Now it's time for diagnosis. It bogged around 3.5-4k rpm, and although I only rode it for half an hour, it got worse. So clearly it is running a lot richer at this altitude (7500 feet) than it did with pods. I'm going to have a look at the plugs, and verify the jet sizes. Some rejetting might be in order as a first step.
The bike ran and pulled really well with the pods, just a little stutter starting off and a little chugging at idle. I could live with both so if it comes to it I could always just throw the pods back on and be content. But I will give rejetting a try, and adjusting the idle mixture. I'm going to give it a 3k-mile tuneup as well.
For anyone else at high altitude, anyone mess with spark plug heat range? I've got either D7EA or D8EA, will have to have a look when I pull them, but wondering if anyone else at altitude has any recommendations. It doesn't ever get too hot here (last year was over 90 for 2-3 days, which broke records, but usually 75 - 80 on warm days, and in the winter down to 35-40).