I recently installed a VAPE conversion on my DT400. Timing should be spot on and it has plenty of power on acceleration. However on deceleration it bucks almost violently. As soon As I accelerate it seems great. I’m wondering if it caused by exhaust back pressure or what else I should consider. Timing is set at spec 2.9mm btdc. It also has died at a stop occasionally. 

The VAPE is firing at all throttle positions and since its clean at accel, probably not spark or exhaust. That said, a good BBQ of the exhaust has many values.

In your case, guessing clogged fuel port on carb or valve, maybe floats too low, possibly idle jet needs cleaning.   

“However on deceleration it bucks almost violently.”

All four of my big bore bikes have that bucking issue on deceleration. I assumed it was just how they are. It’s most noticeable when I’m riding on the road. So I simply pull in the clutch and use the brakes to slow down and stop as opposed to downshifting or engine braking to a stop. It isn’t that noticeable when riding off-road. Maybe I’ll pick the worst one and try the suggestions made by pabdt.

I'm convinced that it is just luck of the draw with tolerance stacking on these. It seems like most of them do it some don't. I'm convinced it's the horrible combustion chamber design with no squish band that is causing it. You can't jet it gone. Changing slides does almost nothing. The high vacuum decelerating is leaning out the mixture enough the bike is detonating, and it can't scavenge the cylinder correctly.

I sent a cylinder and head out to Klemm Vintage to get modified to correct this. But I haven't been had the time to put the bike back together because I bout an XT that is sucking up my time.

Try setting the timing a little more retarded. 2.5mm or so.

You could try going up a size on the pilot jet .
The surging you describe is a sign of lean mixture in the pilot circuit .

I know your feelings, ADGUY. My 400 bucks so bad, it keeps me from riding it much.
It does seem like the engine is staving for fuel. I doubt this is an engineering issue from Yamaha. It is way too noticeable, especially if some big bores do it and some don't. (I have seen YouTube videos of riders on a 400 that don't do it). After reading the Klemm article on air leaks, that is my next direction.

thanks to all for the advice. I have a '74 360 as well and may try swapping the pipe and/or carb to see if the performance changes in addition to following the suggestions many of you have provided. I'll update once I've tested.