I am really curious about the implementation of the vacuum pump ... do you use a PCV valve to restrict the flow, or is there another way to restrict the flow, or amount of vacuum that it can put on the crankcase?
You may not understand what the flapper does, and think that it is doing nothing.
When you are not under boost, the flapper is in the closed position and allows the PCV system to draw some vacuum
on the crankcase. When the intake is under boost, the check-valve closes and that side of the PCV system stops working. With no vacuum getting into the crankcase, any blow-by would build pressure. This is when the flapper is pushed open and the pressure can escape freely and keep any pressure from building. If you remove the flapper completely, the no-boost pcv will simply pull air through from the flapper <- I don't see how the 3/8 hose off pcv is going to draw more flow than the 3/4 hose connect directly to small filter that has to be used on a bottom mount. Conceptually, even @ idle there should be "suction" no? And I'd tee in behind the check valve as shown on the pcv side (see below) & the pcv is still inside of the cap, with no resistance (cannot build vacuum in crankcase). If you remove the flapper, you might as well eliminate the entire low side and go complete VTA (vent to atmosphere) since you would never build any vacuum in the crankcase anyway. Doing that would eliminate a useless vacuum leak.
You are not actually drawing any meaningful vacuum from the air filter assembly, unless you have a significant restriction on the air flow (which I would doubt). The main reason people choose to route the VTA to the filter assembly is to keep it from spewing oil and smell elsewhere in the engine compartment. Any bad smell would be pulled into the turbo and combusted.
For the manifold side to create any meaningful vacuum in the crankcase, you need to have a way to temporarily block the other side. That is exactly the function of the flapper. It allows the "primary" PCV to operate efficiently when the manifold is under vacuum, then switches position, created a free flowing path for when the manifold is under boost and the primary PCV is not operating. Your system would be perfect if you simply put the flapper back in the loop.
I also thought that the flapper was unnecessary and removed it. I attempted to replace it with check valves and learned that the flapper performs several functions (and performs them very well) and it would take a lot of effort and equipment to replicate what it does. It provides a metered restriction to allow the primary PCV to draw vacuum on the crankcase, while keeping that vacuum at a manageable level (not too much). Then it opens, with almost no effort, and allows a large volume of flow to freely pass to keep any pressure from building within the crankcase. The more you know about the flapper, the more you realize that there was significant thought put into designing that part.