jfd, I had one of the first Greddy kits for my 92Si and had similar problems. My fix was to go a little further that you did and get: an EFI Systems PMS piggyback computer, built my own "missing link", and bigger injectors (I recommend 310's). FYI, their "black box" is a "POS". Mine went out early and I was forced to do what I mentioned above.

Since you mentioned that you are running an adjustable (?) B-D FPR with the box, I'll recommend that you keep your fuel pressure static initially and just work around the box issue. From my experience/learnings, all the box does is block an out-of-spec signal from the stock MAP sensor to the stock ECU; some more modern piggyback/replacement ECU's can use the stock MAP sensor up to about 1BAR. You seem to have a B-D FPR, so I'd recommend you just block high-pressures from the intake manifold with a missing link or similar contraption, and just tune your fuel with the A/F guage and regulator adjustments.

I have a Walbro in-tank pump upgrade and agree with all the others that recommend pump upgrades (one in-tank upgrade is better than trying to juggle pressures and pressure-related responses of a couple of differently-rated pumps in series; all I have is the upgrade pump and the STOCK regulator).

Keep in mind that the Greddy engineers were only getting their kit to market to satisfy their own minimal expectations. I've heard of people getting ~10-12 PSI off of the Greddy kits regularly, but everything else associated with the kit (fuel, boost control, blah, yak, blah) should not be confused with stock in these cases.

You mention that you have a Holley-brand regulator vs. the unlabeled-but-still-Vortech-brand regulator that I originally got with my kit. I don't know what your current fuel rates are, but you might want to consider changing from a somewhat-blind FPR arrangement to an additional/adjustable injector system.