Ummm...  why do you have a jumper from the ignition to the lights in the bucket?  Should not be needed at all.

I misstated .  I don't have a jumper from the ignition switch to the yellow light wire.  I ran a jumper wire from a switched ignition source,brown, to the yellow light wire. As I recall, the brown wire was the only switched 12V source in the headlight bucket. 

If you bypassed the rectifier by connecting white and red to each other and connected the two striped greens to the yellow where the original harness connected, there's no reason at all to run any "jumper wires" in the headlight bucket.

The jumper from brown to the yellow you've installed in the bucket could cause a problem.  I don't think that's the same yellow as the yellow from the stator to the light switch.  I can't really tell what you've done in the bucket.

I really don't know what all you've done but I doubt the VAPE instructions told you to install the jumper wire? 

I'm also reluctant to even comment further because I can guarantee you that those scotch lock quick splices will cause issues and not sure what other wiring "shortcuts" may have been taken during the installation or even by a previous owner.

After quickly looking at the wiring diagram, as long as rectifier is correctly bypassed, yellow and green/red should connect together where original harness connected to stator.. This will allow headlight to be turned off by headlight on-off on handlebar. Green/white should not be connected to anything or headlight will be on all the time.

The better way in my opinion is to keep the stock rectifier and connect the VAPE at the headlight and charging wires and not at the battery.  Headlight will only turn on with engine running.  This is a brief description and not meant to be full instructions.

stupid question probably
if you put the regulator at the battery +, will you get more than 12V into the battery to charge it?

"if you put the regulator at the battery +, will you get more than 12V into the battery to charge it?"
No, just 12V.  Connecting directly to the battery as I did was one of the two installation options given by VAPE and the easiest for me to do.
The instructions I received with the VAPE system was for a DT400B.   The application was correct for the DT360  but the instructions were somewhat confusing  as they were for a DT400.