There is not much to say but to start working through the troubleshooting guide you have already linked in your message.
Now, the boost controller, no matter how good, cannot adjust the boost below the wastegate spring level. That level is about 7 PSI. So if you are getting below that, it points to a problem with the turbo system. Unfortunately, you just need to start checking things one at a time. Concentrate on getting the primary boost working perfectly first, and then work on the secondary boost.
Use the overview to see how the components are behaving through the rpm range on a boost run (i.e. WOT):