Go back to basics then. It did sound like an SCV needed a clean, but there are other components that can be erratic particularly if debris has found its way into connectors etc.
If all of the electrical connectors are in good order, you squeeze the throttle pedal and the ECU ramps up the fuel rail pressure, the turbocharger vanes are moved by the actuator to get the turbo spinning faster to provide boost and the injectors simply open and close to let the juice in, combust, repeat.
There are two instant suspects in those that are primarily the cause for this sort of fault: the SCV (which, unless your replacement is dirty, is no longer suspected) or the turbocharger actuator. Your car is identical to mine, and mine has vacuum-operated actuator with pissy little rubbery hoses that go hard from heat after a while, let go of the retainers and allow air to seep in (vacuum is lost = no more workee).
You've said you've been over the vacuum lines, but there's possibly a crack or hardness on some other part of the vacuum line system (it's not just one line that heads down to the turbo, there are other things joined to it). Checking all of it would be prudent.
That's the common stuff. Now for the less common.
MAFS connector. Take it apart, put it back together - repeat 3-4 times to ensure there's no debris in it. You could tell if this were the issue if you used a tool that recorded the MAFS data in real time - you'd see unexplained dips just before the engine "misfired". This would indicate a faulty connection, or a faulty MAFS (and we'll hope it's the connection, the MAFS costs around $400).
I don't suspect the injector connectors. The injectors are working, otherwise you wouldn't get black smoke - black smoke means too much fuel for the amount of air, which is a result of either not reading the incoming air stream correctly, reading the fuel rail pressure incorrectly, or not boosting sufficiently (usually - in the YD25 D40s - that's an actuator issue). It could be reading the boost pressure wrongly too, I guess.
There is one other thing that could cause it - excessive EGR. EGR is designed to dampen combustion. The valve is supposed to be closed at idle and full throttle, it would be interesting to see what would happen if you just blocked the EGR gas path (disconnecting the electronics of the valve itself causes a CEL, I tried that).
Other than that, loose electrical connectors are about the only things left that don't require an expert to pore over the engine.