Pulling and re-dis-assembling-and-assembling the transmission did not fix the problem. But it did get the transmission to a state of being correctly instead of incorrectly (but without apparent functional impact) assembled. I also weighed the CVT rollers on the handy-dandy digital scale I brought with me this time. Just a hair below 5 grams. I'll probably buy either new, heavier rollers for the current CVT, or a whole variator that comes with them already. But not this minute.
My next play was to go to the trash and pull out the stock air box/filter I threw away last night when I installed the "performance" air filter, so I could reassemble and re-mount that.
My mechanic friend interruped that process and asked me to just drive it down the street without a filter at all and see what happened.
The machine ran perfectly.
It also runs perfectly with the "performance" filter connected directly to the carburetor instead of being at the end of a sketchy bit of angled hose.
Adjusted the idle and I'm now good to go again, so far as I can tell. Not necessarily any faster than before, but at least as fast as before. I won't know if the new air setup cured the "starts bogging down about ten miles into long rides" problem until I take a long ride. Which may be in the next 48 hours.
Update: Took the thing out to get a couple of miles of open highway. My speedometer app says it hit 40mph. The previous top speed claimed by that app was either 37 or 39, so I'm in at least as good a shape as before, maybe a little better. The non-RPM-restrictive CDI arrives tomorrow. If it shows up early enough, I'll install it (relatively simple -- pull out the seat compartment, unplug the old CDI, plug in the new CDI, reattach the seat compartment, and go).