Interesting info about the two stage pulser. That would definitly make sence if it somehow got stuck in the advanced "run" mode. 
. Both the pulser, and the stator have slotted mounts. I've considered just fully retarding both, and seeing what happens, but I might try the timing light thing first. 

I guess the switching's done by the box so could the box be faulty--i don't know. I wonder how the pulser tests--ok found the workshop bible. Closest i can get is SC500 motocrosser which is the same full flywheel same pulser. Says white with red tracer to white with green tracer 85 ohms + or - 10%. Sounds a bit light but!!. Probably more important that its not open circuit through it.

Hope ya decomp in the front of cylinder is working as it'll take the sting out of the kick back at least.,

Yeah the specs I found showed resistance between G/W and G/R should be 100 ohms +/- 10%  its 87.5, so slightly under. I've also read they can measure to spec, and still have issues. Not sure on the cdi box itself, I dont have a known working one to swap out. 
 The decompression setup is working well, just did a top end, and cleaned it all up, and adjusted it. 

In one of your posts you mentioned and asked if the terminal on the pulsar is supposed to be bent, NO it should be straight, maybe the rock dinged the terminal? Kinda strange though you said it ran fine, messed with carburetor and then had the kick back. I’ve owned a half dozen DT400’s throughout the years and if it were my bike I would first try to figure out the stock CDI & pulsar set up and my second option would be a complete points ignition set up from a 1975 DT250. Me personally I would shy away from the Rex or Vape setup, they both seem hit or miss on functionality and definitely both seem a miss on customer support after the sale and they already have your ~$400.00.

I'm a bit late to this discussion but have an update on the REX stuff. A close friend locally has installed a couple of these on his bikes - including an MX400 (same setup sans lights). Rex has updated their products and now apparently they are more plug and play at least on these models. I am not speaking from my own experience, but this guy is a vintage racer and a very good mechanic, and he is sold on them.

I may look into one in the future with his feedback.

Powerdynamo/VAPE is very reliable in my experience.  I own several.  I know several others personally who own them as well.  Rock solid system.

There was only one problem I remember seeing here where someone bought a used bike with a VAPE/Powerdynamo unit and it was damaged and missing parts.  That certainly wasn't the manufacturers fault.

I'm a big fan of the points setup as well...  the problem is finding one.  But they are out there.

I would have to take a picture when I get home, but I dont think the bent part on the pulser is a terminal. It definitly didn't have a wire connected to it, nor have I ever seen anything that said it should have. It looks like what you use to set the timing. Line that up with a mark on the flywheel....  it comes straight out the front of the pulser. 
  I've looked into the 250 points setup, and havent seen much available, and what I have seen wasnt much cheaper then a setup from Rex's, and it's still 40+ year old components. If I could find everything I need for cheap, I'd definitly try that out, but for 200+ I dont think it's worth it to me. 

MarkT 
do you know which kit he used? The non adjustable, single source coil? Or the adjustable, dual coil, race version?
  I think the vape system is out for me. I just dont want to deal with changing over to a 12v system, and really not find of no keyway on the flywheel. 

 
not the best pic, but it's what I had on my phone. It's that little tab on the front of the pulser, facing where the flywheel should be. Its bent to the right, and 15 degrees or so.