Finally checked stator, fine. Checked reg/rec, fine. Which means it's in the wiring. (brand new ballistic battery was fine)
Traced all wiring, checked continuity all around and everything checked out. Last idea was the + wire from the main fuse, which is directly linked with the reg/rec via harnesses. I remember I made a new main + wire when I put the battery in the tail section. The wire was one size smaller gauge than stock, but I figured "hell, I'm sure Suzuki made it a size bigger as overkill." Nope. Replaced that with a fatter gauge and all seems to be well now. Head and tail lights are steady now (no flicker), starts much faster (2-3 cranks), and it's much higher volts at the battery than before. (I'm at 13.3-4 now at 5k). Should be good to go now. Lesson: Don't skimp.