If you are still running the same intake manifold as in page 3 of this thread, I'd say that you have a distribution problem.
You may be able to diagnose it in a flowbench, test each pair of runners with the other hole blocked and compare the #'s.
Quick and easy would be a T-section after throttlebody and symmetrical runners to the cast manifold sections.
Extra volume before T-section would also help by slowing the air down for the 90deg turn ahead.
I have ported loads of VW OEM dual port manifolds and it is very easy to get uneven distribution on those, I see a
similarity to your intake runners.
Pekka