Last time I ran into a problem like this on a turbo car (less boost than expected), I found that the vacuum hose to the bypass valve had a kink in it when everything was in place, and thus the valve was not holding against system pressure without the signal pressure on the other side of the diaphragm. This caused the system to run at much lower boost than he had previously run before the intake manifold swap.
The owner said "I already checked that, and it's fine". He was under the impression that it had to be the intake manifold since it was new. I told him that we should just "humor me" and let's swap the entire vacuum hose to the bypass valve, NOT route it the way he previously routed it (so we could see most of the routing when everything was in place), and whala, his boost was back to normal. We then put the old hose back in, routed it the way he had previously routed it, the problem returned. The hose had been kinked (out of view once everything was secured and routed), causing the issue.
I also found the issue on a different car a year earlier, but that one was a nick in the vacuum hose going to the bypass valve instead of a kink, so it was an even easier diagnosis.
Not getting full pressure to the correct side of a bypass valve is one of the more common reasons for the symptoms you are expressing. It's also one of the more overlooked.
Just some food for thought.