I am not a mechanic and could be wrong but heres what I think is happening.
The injection pump relys on pressure from the turbo to puch the diaphram and delivery rate rod down, this increases fuelling and boost increases giving the right mixture, clever huh.
So at the point we are getting lumpy running tells me there is either not enough fuel to air or too much fuel to air. It is probably not enough fuel to air as you say the fuel is thicker and will take that little bit more of a push to come through and so at that precise point the boost is supposed to help the pump there isnt enough boost at that rev to deliver enough fuel.
See I have a boost gauge and EGT gauge and tuned it to its safe potential, and the judder I feel is only when revving not in gear, when in gear and under acceleration I dont feel anything. You could try and turn your smoke srew in half a turn and see if that helps, maybe adjust the diaphram a couple of degrees to get that extra fuel in before boost takes over.
Jay