I found the cause of my electrical woes... Turns out 16' TT250 was right about the voltage regulator. The connector was just barely disconnected, it looks like it may have separated because I didn't give the wires enough slack when zip-tying. Lesson learned: give the wires slack when rerouting
When I went over a bump or something the connector must have came loose. This fixed my blinker issue as well, and now I have a battery voltage jump when I rev the engine... awesome.
So anyone having issues with funky blinkers may want to check the voltage regulator connection.
Now that that's taken care of .... time to install the new pipes and jets.