i dont see how the map reads manifold vacuum correctly if its on top of the blower.
it is under the throttle butterfly, there's always vacuum there unles you press the gas pedal.
the bypass valve should open when the throttle is closed and should progressively open based on your throttle opening, the vac line for that valve should be connected between the t/b and the supercharger, not after the s/c (just in case you want to check) - things that can go wrong with it: vac line connected in the wrong place, tear in the membrane (not working/not holding vacuum), bad pressure (vacuum) setting on it if it's adjustable.
I'd put the stock injectors back on and test again, then if all good add the FTC back on. What if the injectors are not compatible, just taking a wild guess here - are you sure they are high impedance? what about the size (lb/hr)? or maybe they just squirt like crazy. you have a set of 24lb/hr injectors, that would be the next thing i would try once you tested the stock injectors and maybe after that if all checks out go on a junkyard hunt for larger ones.
seems that you're on the right track now, just keep eliminating possible problems until you get to the root cause - don't try and jump ahead though, 1 step at a time.
if it still does it with the stock injectors then the next thing is the supercharger, intake, fuel rail assembly (put the stock ones back in) - worst case scenario (or maybe best case scenario depending how you look at it) will still have the same issue once you return all back to stock which means then it's something unrelated to FTC/Supercharger/Intake/Fuel Rail/Injectors. Keep at it, you'll get it resolved, you already won a battle by eliminating FTC as a possible issue.