If the A/F's are 10.0:1 @ WOT...
10kw is not really a huge ask from a B16A as far as power gains go...
There is most certainly 5 of those KW right there...

The other issue could be the cam timing is different now if the head has been shaved.
This can cause a general loss of power accross the rev range.
Retarded tends to lose power everywhere but still have a good curve.
Too far advanced tends to increase mid range at the expense of top end.

To see a benifit from the use of the manifold & throttle,
You will likley need to have the ECU tuned to suit your car.

Re A/F's
Are they rich everywhere else also?
That being the case, a change in fuel pressure could sort things out.
If it's only overly rich at WOT, the problem is likley what I said in previous post.
With change in manifold absolute pressure due to larger throttle & manifold.