In regards to the boost problem.

The stock intake manifold has a few issues.

Theres a vacuum line that feeds from the intake manifold to the firewall, not sure what this is for, I'm going to assume it feeds actuators for the climate control (as i havent looked too much into it yet) also, the brake booster line could be an issue, as a lot of times the brake booster itself will actually leak and the fitting where the line comes into the booster will leak as well

Also, where the arm for the butterflies comes through the intake manifold to the vacuum actuator, the only thing sealing around the shaft is a hard nylon bushing. This seems like an issue, it might seal under vacuum but the positive pressure could cause the bushing to unseat, plus the added heat from the intake charge could cause the bushing to expand at a faster rate than the shaft causing a gap to open up.

I've been looking at the stock intake manifold for my turbo setup and honestly it has lots of issues. You already addressed the egr problem.

The other issue is i'm assuming you've fed the butterfly control actuator vacuum from the intake pre-rotrex.... If not the butterflies wont close/open under load as the actuator wouldn't see vacuum.