Joining here late... certainly not claiming any superior knowledge on this...
...but...
I don't think your system is ANYTHING near efficient with the combination and problem description you are giving... and I FURTHER agree with the opinions that you are "falling on your face" (term meaning = vehicle "loads up" and loses power...).
1000cc injectors????? WHY!? (for 400HP ranges, anyway...)
I am a "lowly" 440cc setup, but able to push 16psi very HARD... and I had to "back off" the GAIN on my VPC to keep from "LOADING UP" my fuel. (I can BOOST to HIGHER levels... but I believe I'll be 100% cycling my injectors... a recipe for LEAN DISASTER!) My car is pretty efficient, as I am ABLE to obtain around 28MPG if I use BOOST very modestly for a highway cruise... (even boosting alot... I achieve better than 20 no problem.)
I think your "fuel dump" into the cylinders is "overwhelming" the motors ability to burn a cleanly atomized mixture... check a plug. (Mine burn a tan color... and I blow very little "boost fart black smoke" when I "hit it"... a good sign, me thinks.)
Can you DIAL DOWN your fuel delivery (GAIN) as it comes on the boost? (and if the plugs are "fouled"... black or wet, even... I'd put a fresh set of quality... NGK, Denso and the like... although personally, I like the Silverstone Beru plugs.)
Good luck, man.
-crisp