Well, ran some tests.
Pulled the steering wheel and inspected the switch, switch is fine.
Disconnected both the switch connector and the flasher, Ammeter still did the wave with ignition in both ACC and ON. Found a broken wire on the switch cables after the disconnect. The orange wire to the gear selector light. My wiring was shoddy on that one as I had limited wire and it already had splices in it and moving it around separated the wire in the crimped splice. That isn't the problem, but it is a problem.
The round fender light on drivers side wasn't working. Works on passenger side. Disconnected it to isolate it and the ammeter still did the wave in both ACC and ON. Possibly a short in the line before the bulb?
Tried it with lights on and off, still had the issue. Turning on the lights dipped the ammeter well into the discharge side and still did the wave in both ACC and ON.
I put the charger on the battery. It's currently reading 13v and 1.25a.