try connecting the vacuum lines the other way around?
Sorry, not sure about ECMLink. Maybe Scott G?
The wastegate needs pressure to open, so to open the ECU needs to have the solenoid allow pressure from the source(intake manifold) to get to the wastegate diaphragm.
To test the rest of the system, (turbo, intake, exhaust etc), just run a vacuum line from manifold pressure straight to the wastegate. Stock style wastegate should open around 8-10 psi, but with a 3" exhaust it will probably creep up higher.
most 16g actuators are a couple of pounds higher so you should see 10 or so psi.
Then I would put in a manual controller and see if it can raise boost normally.
If not, you have to figure out what is mechanically causing low boost. Usually either an issue with the turbo or an exhaust restriction, but it can also be an intake restriction(rag in the airbox etc), or a huge loss of boost somewhere. You won't notice it on SD as it will still run fine. Remember you did ding your intercooler on the curb at my shop that one day? If you split a weld or something that would account for it. I just did a quick visual inspection as we were on the clock, but you should do a boost leak test.
If boost raises normally with a manual controller, figure out the solenoid and the 'Link issue