Hey Mike,
I've been round and round with this. Not sure about the VEC II with a Paxton, I really don't have any expericne with it. The split second box is actually program-able and a very good piece in the right hands. I run an AEM with two external 400 LPH Bosch pumps and one internal high volume Walbro that keeps the fuel module full, but my car is a darkside Paxton car - over 1000 hp on pump gas.
I would need more info on your engine to help, but I would suggest you use the stock Paxton set up if your car is stock with only a Paxton. I think the two Paxton supplemental pumps are 250 LPH each, so you are not getting enough fuel. This is fairly obvious by your comments on fuel pressure. My fuel pressure is set at 67 psi, vacuum modulated down to 55 at idle. Under boost my Aeromotive fuel pressure regulator increases fuel pressure on a 1:1 ratio with boost, so at 10 psi, my fuel pressure it back up to 65.
Fuel volume is also important and again I would guess that the two pumps that come with the Paxton supply more volume too.
You didn't mention your Air/Fuel ratio's. What are they doing with increases in engine speed?
Be very careful with this or you could be rebuilding your engine.
Good luck,
Dan