Pulled cap/rotor. Noticed they were now burnt a little. Sanded them down and it fired up. Ran good for a couple minutes then started missfiring and died. Replaced them and it started right up and ran great! Then started missfiring after about 10 minutes. I'm thinking that my secondary problem was the cap/rotor, and my main problem is likely the plug wires. Possibly damaged and causing the cap/rotor to work too hard. Its still running really good, but at idle I can hear often a missfire. I'll replace the plugs and wires this weekend, and clean the cap/rotor again.
I've never heard of or experienced an ignition failure like this. When I put the motor in the plugs, cap, and rotor all looked really clean or new. That's why I never suspected these as the culprits. I'm happy I made tons of progress, unhappy at how much time I spent chasing ghosts.