Here are some pics I took of the wiring going into the boxes.
Well, the pictures solved one mystery, but not an important one. The blue wire mod was not done correctly, but in my opinion it has been done better! With your current setup, your tail light and dash are controlled by your tail fuse, and your headlight is controlled by your headlight fuse. (normal blue wire mod leaves the headlight controlled by the tail fuse, and the tail/dash is only protected by the main 30 amp fuse, and the headlight fuse is unused).
Unfortunately, all of those things have no power when the ignition is off, so there's no chance of a vampiric drain BECAUSE of the wire swap.
You said the drain goes away when the 8-pin connector is pulled from the box. The ONLY thing not completely de-energized on that plug when the ignition is off is the R/R. I bet if you unplug your R/R next time you stop, your drain will be gone. If so, time for a new R/R for sure, and hopefully your stator is still ok? Best to check the AC voltages on the yellow wires just to be sure.
Chances are that one of your stator windings is shot (probably the winding that used to turn your headlight on). $400 is a great deal if the mechanic understands that they're splitting the case. Otherwise your $400 might quickly balloon into something much bigger.