Haven't posted here in a while but I rode my 250 in a 100 mile vintage endurance race about 5 years ago and swamped it during a river crossing.  I got the bike dried out, oiled up and finished the race even if I was dead last by hours.  Bike ran flawlessly but once back home it never ran again despite new coils, plugs, points and condenser.  So I ordered a VAPE system from HVC Cycles but it sat on the shelf for all those years.  Last week my brother and I installed the system and everything worked well except the turn signals and kill/key switch.  At first the bike wouldn't fire at all then my brother disconnected the blue wire from the black/lwhite stripe wires from the key/kill switch.  The bike started first kick and runs stronger than ever but not I can't shut it off other than reaching under the tank and grounding the blue wire to the exhaust pipe.  I asked HVC for help, since I bought it from them, but they told me to get a schematic and figure it out.  I have the factory service manual and have downloaded all the available schematics from this site and my electrician brother can't figure out where the problem is.  Today we went back and retraced every wire on the bike and ran voltage and continuity readings and everything seems up to snuff but no luck shutting it off via kill switch or key. 
Does anyone have any useful suggestions?  I have a handlebar mounted kill switch to put on it and it does work but I'd really rather use the ignition key to stop it. Thanks for your input.

Black/white that went to original ignition coil should be grounded with key off and/or handlebar switch off. So you simply connect the black/white to the VAPE kill wire.

That is unless someone has hacked a bunch of wires during the install which I've seen several times. Probably because the instructions are not that great.

Make sure both factory switches are on and the black/white should not be grounded.

Thank you both for the input. The black/white wires from the kill/key switch were not messed with during the install. They are joined together in the OEM harness and are working correctly when tested with an ohm meter. However, when I plug the blue wire from the VAPE coil into them the bike won't start and when I unplug the blue wire, as suggested in the not so clear instructions, the bike runs great. I'll do a little more digging and troubleshooting and see what I come up with, and as usual it will probably be something simple. It does make me a little nervous though as next up on my lift is a VAPE install on my RD400.

RD is battery ignition so VAPE ignition kill is not as simple. 

Not sure what your problem with the DT250 kill is...  I am wondering if it's why it stopped running with original ignition? 

Not sure how the wiring could be "working correctly when tested with an ohmmeter" because it seems to grounding the blue when connected?  Otherwise you wouldn't lose spark.  Might be the test method?  Hopefully you'll find the problem quickly.

The instructions from Vape are terrible......

The only way I was able to make it work on my CT3 was to install a kill switch on the handle bar and connect it to the blue wire (same principle as touching it to your exhaust pipe).

(MarkT helped me through the install issues that I had)

On a Yamaha magneto model (all Enduros except the 125 electric start models) if the key switch (and on later models, the kill button) black/white wire doesn't work to shut off the VAPE then there's something wrong with the key switch, kill button, or wiring. 

That wire should be "open" with key on and grounded with key off.  No "relays" or other BS needed on a magneto bike like some have reported reading in the instructions.  Just one simple connection to the VAPE blue kill wire.

Something else I've seen is someone inexplicably connects the original points wire that went to the original stator (and/or the "timing check" pigtail on some models) to ground when installing a VAPE. 

Posted a reply a couple days ago and for some reason it didn't post, probably didn't hit the send button hard enough. But I found the issue was as Quartermaster35 suggested. Again ran a continuity test with the ignition and kill switch on and had good continuity (coil not grounded) But when I turned the ignition switch or kill switch or both to off, I had only 0.006 ohms to ground. So I figure when I swamped the bike those years ago I have a good case of corrosion in either the switch(s) or wiring connectors inside the headlight bucket. In either case, I wired a handlebar mounted kill switch and all is good now.
Thanks to all for the good constructive advice and help with the trouble shooting. Now if you'll pardon me, I have some miles to put on the DT...we have a lot of catching up to do.

Glad you found a solution!  I do have to say your "troubleshooting" doesn't make any sense to me. 

At least twice you said the bike won't start with the VAPE blue plugged into the stock black/white switches on or off so you had to leave it unplugged and reach under and short the blue wire to ground   This indicates the black/white is shorted to ground all the time.

Now it sound like you're saying the black/white is open all the time due to suspected corrosion in the switches?  Which is exactly opposite.  

Anyway, if you want the original switches to work, it shouldn't be too hard.  Yamaha switches are pretty robust and kill is just a simple on-off circuit.