For those wondering what I did a few months ago after receiving feedback in this thread.  I took the advice of many and left the top port open, and allowed the N75 to manipulate only the bottom port.  This is a much simpler configuration and allowed better control of the wastegate from what I found.  I did need to heavily modify KFLDRL and KFMLDMX (basically had to tone them down).  Eventually I'd like to perfect the PID so part throttle boost delivery is cleaner, but it works for now.