Further to the process above I've done some more work on this problem as it seems we're often confronted with a turbo that's been fiddled with in that both the stop screw and actuator length have been changed.
This process laid out below seems to have worked well for me on my YD25 in the Thai 2011 D40. It's a good way to get a starting baseline if you're not sure what's been adjusted before. You need a vacuum pump with gauge, an 8mm ring spanner modified as described above and a long ball ended 2.5mm hex key.
Remove the three 10mm bolts securing the turbo heat shield and push it towards the firewall.
Loosen the lock nut, back out the stop screw so the lever arm can't touch it and use the vacuum pump to lift the actuator rod as far as it will go. This closes the variable vanes.
With the vanes still closed wind down the stop screw until it touches the lever arm then wind down another full turn and temporarily tighten the lock nut and mark the screw with a paint pen for a reference. I found this bit of information on a non English speaking forum. If I can find it again I will post a link. This initial setting and reference ensures the vanes never fully close which can damage a VNT turbo.
Adjust the rod length until it just touches the stop screw at 18 in.Hg. Use a thin strip of paper as a ‘feeler gauge” so you know when it contacts.
Road test with a boost gauge or Torquepro connected and you'll probably be moderately over boosting. This means boost will climb quickly and keep going until the ECU steps in and the boost will suddenly drop.
Loosen the lock nut and turn the screw down another ¼ turn down and road test again. In my case it was still over boosting but not as much.
I adjusted the stop screw a further ¼ turn down and road tested again. This time it would get to 18 to 20 psi and hold that pressure. Before the ECU would suddenly step in to cut it.
Individual YD25's may need the screw turned down a bit more or a bit less.
I checked the actuator rod again and it was still hitting the stop at 18 in.Hg or a smidge lower. IDparts (see video from 3:44) say 15 to 18 in.Hg is acceptable with 18 in.Hg being on the "safe side". Considering the accuracy of the gauge and the method of setting there's a bit of leeway with the rod length. As long as the lever hits the stop screw at around 18 in.Hg or a bit less it works. Remember the boost control solenoid is modulating the vacuum to the actuator in a closed loop to keep the boost within target settings so that rod is jumping up and down all over the place.
So I have the stop screw 1.5 turns down from when it first touched the lever arm with the vanes fully closed and the lever hitting stop screw at 17 to 18 in.Hg. It's running well.
Video from IDparts on how to adjust the rod length on a Garrett VNT turbo. Watch from 3:44