Finally had a break in the rain while I was home and did some tests. I believe the rec/reg is the issue even though I measured good and equal continuity from the plug.
I am getting increasing AC voltage from the 3-wire plug directly off of the stator as well as the plug that goes to the reg/rec. New stator is definitely working! The only DC voltage I get is from the battery, which runs the bike until it cuts off at 12.5V or 12.7V due to the BMS system in it.
@TallTom I removed all fuses, cleaned up the contacts with sandpaper, and reinstalled only the "main" fuse by the battery+ignition+fuel. No change, but great idea to test.
Since I paid big bucks for the lithium battery, I am looking at getting Rick's hot shot reg/rec specifically for lithium batteries unless anyone says otherwise.