There are many things that can affect boost, you have already covered some of them.
First I would see how much vacuum I have at the turbo controls, a small vacuum gauge with some tubing and a Tee can tell you this.
You should have full vacuum at the vacuum solenoid and at the turbo modulator valve when the key is on and engine running.
Then I would test to see what vacuum you am getting at the turbo vane controller AT the turbo when accelerating and getting the low boost numbers.
If all that looks good, I would install a mechanical boost gauge to compare it to what you are seeing electronically through the ECM.
Remember, the MAP sensor is supplying those boost numbers, so if the MAP is giving the wrong signal to the ECM, it will affect everything with the running of the engine.
You said it was EGR deleted, so is the FCV removed? If it is still on the engine, the butterfly may be stuck partly closed limiting boost.
If the boost is actually low and it is getting normal fuel levels, you should be seeing lots of black smoke when accelerating uphill with those low boost numbers.
Boost hoses, CAC leaks, must be ruled out!
You got to start ruling out each system one at a time to figure out which one is causing the problem.
Wish you were closer, I could help in the testing, I have the equipment.
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