Boost aside, it sounds like you're having either motor problems or a faulty boost gauge. A non-boosted car should hit 0 vaccuum as soon as the driver hits WOT. Are you reading the gauge at partial throttle or WOT? You won't make much (if any) boost at partial throttle.
TB spacers are a waste of money. Slap a gasket and some RTV between the TB and the TB bracket and you're good to go.
No, it doesn't effect the supercharger, but ANY check engine light will cause the car to go into a "safe mode." This means the car will retard timing approximitely 5 degrees and you will lose power.
Yes, a small piece of tubing that can handle high pressure will be used to hook up the boost gauge. Since many people get rid of the black box eventually in favor of real tuning, most opt to use a different reference line. But the black box line (if hooked up correctly) should work.
If the belt is slipping (which yours is and it will only get worse) then yes. A lose belt will cause the belt to slip and not properly spin the pulley for the supercharger.
You need to read this: http://www.fordracingparts.com/rbr/tech/files/FRPP_JRSC_Belt_Details.pdf and follow the directions. You have the new alternator bracket and should be using a different belt routing.
As long as it's not broken (which it sounds like yours might be) it should work fine. Hell, if you're that worried about it shoot me a PM and you can have one of my spares, just pay for shipping.
Something is wrong somewhere. It sounds like your boost gauge isn't hooked up properly. Since your gauge and black box are hooked up to the same reference line... your car coul have some problems if the black box isn't working. If your car is showing vaccuum when you're in boost, the black box will not send extra fuel to the engine and you could blow the motor.
Stay out of boost and try to figure out the problem. I'm betting something is hooked up wrong.
Nate