I'm installing a VAPE system on my '72 DT250. How and where would be a good place to install the regulator? Also do I need to remove the silicon rectifier?

Thanks,
David

The VAPE wiring instructions might be really bad...  I worked with the original owner of the company before illness forced sale to VAPE.  The kits were developed for many brands and models to mechanically install a "new heart" (ignition system) onto an old machine.. 

With so many different models, Edgar's original wiring diagrams were very generic and basically just identified the Powerdynamo/VAPE wiring.  It was up to the installer to adapt the new ignition system wiring to the old bike.  Since then, VAPE seems to have some "model specific" instructions that are sometimes terrible for the Yamaha Enduros.

Some pointers:  The ignition section of the VAPE is pretty much standalone.  Wires just go from the stator to the combination ignition coil/CDI box.  For magneto bikes like yours, the original black/white kill switch wire simply connects directly to the VAPE kill wire out of the coil.  YOU DO NOT NEED A RELAY even if your instructions say you do. (Relays are only needed for bikes that were originally battery ignition like the 12v electric start AT1 Yamaha) 

The regulator output wire is generally shown connected directly to the battery in the instructions.  For several reasons, I don't do it this way. 
An easier and (arguably safer) way to wire it in my opinion and experience is to simply connect the 12v VAPE regulator output wire to the 3 "power" wires that connected to the original Yamaha stator.  A simple pigtail can be made that connects the VAPE regulator output to the harness Yellow and both Green wires right where they plugged into the Yamaha stator...  one wire from VAPE to all three harness wires. 
This simple method lets the Yamaha system function exactly like it did before the conversion and can easily be made "plug and play", no need to cut or modify Yamaha harness to install the VAPE.
You mentioned the stock rectifier...  with the method described above, you may leave it in place.  If you remove it, you'll need to connect the red and white to each other and insulate well. 
With the stock rectifier bypassed using the wiring method above, the headlight will operate with engine off, with rectifier left in place headlight will only work with engine running as it did stock.  Not critical on your model as headlight is key switch operated... 
(On later models with the "always on when running" headlight you must keep the original rectifier or add a headlight switch of some kind.). 

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Notes below are ONLY if you decide not to follow the above advice!
If you decide to run the VAPE regulator output wire directly to the battery, protect it well and add a fuse.  You'll also need to get the Yellow that went to the original stator connected to the battery somehow (or you won't have a headlight) and it also needs to be fused.  The green wires that connected to the original stator next to the yellow are taped up and not used.  Original Yamaha rectifier would need to be removed and red and white wires that connected to the rectifier must be well insulated so they can't short to ground.  (Headlight will come on without the engine running with this method.)

Thanks for the information. It is very helpful and explained a bit better than the instructions that came with the VAPE system.