Outa my league now you've gone 12 volt & DC lights. Is there a fuse involved. If you want to run lights off the battery at least find a live wire out of the ignition switch [im guessing] & that live i'd think should head over to you're light switch on the handlebar. Don't read too much into my post as i know Mark & others are onto it.

Alrighty, here’s some photos of my vape 12v wiring, it ain’t perfect I know, and in the meantime I’m just trying to get the headlight and gauge lights to work. 

imgur.com/a/05MeYlj


 

Nice pictures and explanations!  Hopefully below is your picture of the now unused original stator wires.  Yes, if you connect that light blue to the neutral switch on the case the neutral light will work again.

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On the headlight....  did you remove the stock rectifier under the tank that had a white wire and a red wire going to it?

You've mentioned having the wrong handlebar switch...  have you solved that issue/question? 

It will be very simple to get all the lights working again just like original if the original rectifier and headlight switch are okay. 

Hey Mark, yes, I did remove the rectifier under the tank that connects to the red and white wire. Should I have left it? I'm sure i still have it in the parts bin if I need to put it back. 

As for the handlebar switch, I did have the wrong one! However, last night I cleaned up the old one internals and transfered them to the new shell of the wrong one and wired it up and I got most things that weren't working to work. I wired up the neutral switch wire as you suggested and it works perfectly! I also finally got the flashers to work with the flasher relay. As of last night the the headlight still isn't getting power, checked to see if I got any power via kicking it over and no dull glow or anything, checked the wires same way via multimeter and I confirm no power. 

Alrighty, I tried hooking up the old one via red to red and white to white and grounded it, and it didn’t change anything that I could tell, I also tried a new one but didn’t ground it on the frame via bolt and nut which I’m not sure if I need to for it to work? Anyways curious what you folks think 

If ya talking the original rectifier--you refitted--they're not grounded [just mounted] as such & change ACvolts to DC amps? 'MarkT' help me haha. Don't let me sidetrack you. Mark possibly meant if its 'off' then leave it 'off'.

Are you still trying to run your lights off the mag--not battery.

Whoa!  Back up the bus.  I was asking about the rectifier in terms of rewiring the VAPE to work as original..  Installing it on its own doesn't "fix" anything.  But it will be needed for the new wiring to work like it did when it left the factory...  which is how I wire them.  (I will post another option after this one.)

In that connector where you found the sky blue, you will also see two greens (with stripes) and a yellow (looks like it has a white stripe).  You will be using those wires. 

Since you had some potential issues with the original switch, I would suggest getting a fuse and holder with a 10 or 15 amp fuse for added safety.

Step 1.  Remove the VAPE red from the battery positive post.  Leave the original red wire to the Yamaha harness connected to the battery.

Step 1a.  Add a fuse and fuse holder to the end of the VAPE Red.  (Optional, but a very good idea.)

Step 2.  Make sure original rectifier is installed and connected.  (Rectifier does bolt to frame but red and/or white should not be grounded.)

Step 3.  Connect the Yellow/White and the two Green wires to the Red wire from the VAPE.  (Hopefully you added a fuse holder to the VAPE red so this connection is fused)  So you'll have a total of 4 wires connected all together.  VAPE red (1 wire) and the Yellow and Greens (3 wires) in the photo below all connected to each other.   Note the Sky Blue goes to neutral switch and the black/white is not used.  Just tape up the black/white.   Please ask questions if this doesn't make sense.

DONE!

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I can give you the theory of how this works...  most important question you might have is about the rectifier?  Rectifier is just a diode...  think of it as a one way valve.in a piping system except it only lets the current flow one way.

The two greens were the original battery charge wires.  Depending on whether the headlight switch is on or off determines which green connects to the rectifier white wire.  We don't care because the VAPE is providing a nice regulated 12 volts so we just connect them both to the VAPE.  The stock Yamaha rectifier will allow the power from the VAPE red to flow towards the battery and charge it when the engine is running.  The rectifier is there because we also have the yellow connected to the VAPE Red.  The stock Yamaha rectifier will prevent the current for the battery from powering the yellow.  So with the rectifier in place, the headlight won't work unless engine is running.   Everything will function like stock.

Scribbled Wiring diagram:








 

Another option is to leave everything as you had it.  No Yamaha rectifier installed (make sure Red to rectifier is taped up!!!)

Leave the VAPE red to the battery. 

Now simply run a jumper from the Yellow/White (the one in the same connector with the Sky Blue) to the battery positive post.  Now the headlight will be controlled only by the headlight on-off switch on the handlebar and you'll need to remember to turn it off or battery will go dead. 

Another option is to run a jumper from the yellow/white to the solid brown at the turn signal flasher.   Now the headlight will only come on if the key and the headlight switch are on. 

I don't use either of the above methods...  I like the stock arrangement of headlight coming on with engine.  I know someone who said connecting to the brown burned up their key switch after a while...  and others who connected to brown and never had an issue.  (I think the guy that burned up key switch was running a high power headlight) 

Would [could it work] a regulator rectifier with only one wire as shown.
Or is it just an AC regulator only. Just asking.
I'm electricaly challenged at the best of times.
Would you normaly have a fuse 'there' [does that make it a fuse on the AC wire.
Does say Red which would normaly be DC though.

You can tell i don't know what im talking about!! mostly.