The bypass valve is vacuum driven. When it sees vacuum, it should be open; when no vacuum is present, it should close. My experience with the blower is on my 3V with the DOB setup and there is nothing but a vacuum line from the manifold to the BPV. I don't know if there is a more complicated setup with the GT500 setup, but since lack of vacuum closes the valve, I'm not sure how there would be electronic overrides (I certainly could be wrong). I assume you've checked and double checked the vacuum lines?
BTW, awesome build! I haven't been on this forum a lot but I have been following this build. Nice job!