Ok, so did some more looking into it. I'm fairly certain the battery is not the issue here, I checked the voltage again at various points. From a cold start this morning (been off all night), the battery ready 13.09v terminal to terminal, 13.09v terminal the engine ground.
I applied full choke, pushed the starter for less than a second and she started right up with no issues. After warm up, idle battery voltage was 13.5v. I revved up to 5k RPM, battery voltage was still 13.5v, but slowly climbed up to 13.65-13.75v. All of the readings here are battery to engine ground / frame.
Finally, I turned the engine off. Battery voltage dropped to 13.31v. I let it sit for about 60 seconds and tried to start her up. This time, I had no choke applied (the bike was warmed up and running for at least 10 minutes), and I did not give it any throttle. The starter just turns over, and over, and over... finally caught after about 4-5 seconds and started up. Battery voltage during the starter cranks was 10.85-11.0v.
After all this, I took her around the block a few times to warm things up even more. I pulled back into the garage and left her running. Battery voltage was 13.55v at idle. I turned the engine off and let her sit for about a minute again. Same as before, no choke applied, no throttle, just pushed the starter. This time around, she never started up. Just turned over and over, backfired quite loudly and never caught. I finally gave up after about 30 seconds, didn't want to drain the battery.
I let her cool down for a good hour and half and tried starting again.. full choke applied, no throttle, starts on the first crank.
Clearly something doesn't like being warm. My R/R is in the stock location, considering moving that tomorrow. I also took the battery in to two different places (O'Reilly's, and then to Advanced Autoparts, because the O'Reilly's guy looked like it was his first day); the testing equipment at both shops reported the battery to be in good to excellent condition. It's a "MagnaPower" 220 CCA sealed AGM battery, if that matters.
Plugs are brand new, though I used the existing wires. Otherwise I have not touched anything with the electrical system.