A very common problem is the plug going to the VR oft times contacts lose tension or wires internally break...what is the charge voltage with the VR installed...it should read 13.8-14.2 VDC if the battery is fully charged. If you pulled and load tested the battery using the external Battery Tender harness to charge battery directly on the bench to full float voltage, it should read 12.8 to 14.2 (a higher number is because you just take it off the charger).
Install the battery, aim the headlight at a blank wall...and hit the starter, the headlight if it dims more than 1/4 Brightness to totally going out...your battery surface charge/reserve is insufficient (this is your online battery load tester) once the engine starts (if voltage drops below 9.5V ignition power will be insufficient to start the bike). If voltage stays at 12.6 and starts dropping after running, the charging ckt is not able to keep up, and so I would suspect the VR unit first (it is also the easiest/cheapest to replace. Then I would pull the primary cover and take a whiff...if it smells strong/burn varnish, your charging system is suspect.