The with the stock turbo and boost control, the boost tends to spike on when getting into boost. If you over boosting, using the stock ECM boost solenoid. If you want to use the boost controller and turn the boost down, I would adjujst the wastegate rod to stock specs (3/4 of the pin overlap) and then adjust the boost controller.
Rethinking what I wrote.
I would adust the wastegaste to factory spec and turn the boost controller all the way down (ie so it's running 8-9 psi on the wastegate.) I would slowly turn up the boost controller and monitor the boost level and spikes (prefereably with a scan tool). I would guess you can help limit the boost spikes by lengthening the rod but it will sacrifice spool up. You will probably have to compromise a little.