I just had the same trouble pretty much after a small hard plastic bit of vac connector fell into the front entry of my turbo.
Drove alot like you are.
No boost. Hard accel my guage showed it go up to 3-4psi.
A few drives like this it slowly got better, but not much. I could get up to about 5-8psi & after slugging along near or actually redlining 4-5000 then in 4th getting about 2-3psi.
The actuator arm had stopped bobbing up and down at idle.
I had full spools & overboosting when vac to actuator testing & using my boost gauge did a few 10-ish km drives feathering accel not letting it overboost over 25-max30.
Them i would drive 10-ish km home hooked up normally.
I ran 2 x 500 bottles of Nulon Turbo cleaner to 40l of fuel a full bottle.
It was blowing alot of smoke, gradually slightly improving boost back up to about 8-10, even 12 in second gear... Then after a freeway run when actually getting up hills at 90-100-110 again but using alot more engine (and ALOT more fuel due the turbo issue and higher revving, smoke blasting out greyish with the cleaner or even quite black unburned fuel) i got up to about 15+ psi at best on a 100km motorway to home run.
Everyone here etc said if i have mad boost plugged straight vac to actuator (& the actuator arm was going straight up when fitting it that way) its gotta likely be a dead solenoid. Bcs.
My new one arrived & i was fixed straight away in 5mins!
21psi, turboing lovely.
Utes fast!
I can say that i once bought a bcs a year ago when i first got the vehicle to try out whej was running bit rough n smokey etc etc & that BCS Seemed to be dead on arrival.
In hindsight maybe the electric connector wasnt oushed in quite hard enough where it snaps in with a good click & then u should push it some more and make sure its tight.
Possibly your new bcs is dead on arrival or it just isnt clicked in right or tight enough at the connector.
Mines an 07 Spanish & the $25 BCS i just bought off ebay worked perfect on fitting & i believe might suit every model of D40 2.5 motor, there's at least 3 part numbers covered in the eBay listing.
Old Tony here said that my cheap BCS should be as good as any.
Try check your bcs as i described,
Or buy another and try that.
When u said now u have good boost on the direct vac to waste connection, that in theory might be saying what another just said, the actuator arm might be undone..
Or it could have been sticky.
The turbo cleaner fuel treatment helps with that & the exhaust side of the turbo to clean carbon and stickyness away & might help the turbo back area spin better also i guess. Worth a go. Only $20-30 a can. Run full can to 40 litres diesel for best clean effect.
I think if you do that plus now you are seeing boost now on yr direct connecting, checking the electronic connectors to yr bcs are good,
Or another bcs in case u got a DOA one might solve it
I'm looking for I have seen that 
