98 GTP Boost under 50%

I have a 1998 Grand Prix GTP. We just replaced the engine with a long block, Supercharger was replaced about 20,000 miles ago (prior to the new-long block). The old engine, which had over 250,000 miles on it, prior to eventually failing, always got around 28 mpg on the highway and went 0-60 in the low 6 second range. The new gets 3-5 mpg less in the same conditions and has FAR less power (it feels like around 80hp less out of 240). 0-60 is now around 9 seconds.
We first suspected the problem was the new long-block. A compression check showed cylinders from 90-130 psi and the engine stalled constantly, re-manufacturer agreed that these symptoms warranted an engine replacement under warranty. We sent the engine back and they rebuilt it again (they did not say specifically what they did just that they did rebuild it again) and sent it back to us. We reinstalled the engine again, but, now there still is the same low power and poor fuel economy after reinstalling the engine again (the engine no longer stalls after the 2nd rebuild).
I now suspect the problem is the supercharger. The boost gauge never goes above 50% and rarely goes above 25% regardless of load. If I remove and plug the vacuum hoses (either side) of the boost actuator valve so that I force the bypass valve either open always or closed always there is no change in performance under either setting. With the bypass valve always open or closed, boost still shows 0 until around 4,000 rpm where it may blip up to 25% or so and the engine may hit 50% if I am lucky redlined. This makes me suspect that the supercharger isn't working at all...but this doesn't make sense since it is not seized up and did not appear to be broken when we installed it either time we installed the long block.
I did notice some scoring on the blades of the supercharger before we installed it on the new motor. But, they looked very limited...and the blower was remanufactured 20k miles ago and makes no unusual noises.
I have no trouble codes.
We installed a brand new MAP sensor and the MAF sensor is only a couple months old. New MAP sensor made no difference, however I did notice that if I remove the harness from the MAP sensor the car shows more boost, almost reaching 100% on occasion, but there is no noticeable increase in performance. Boost reads identical with the old MAP sensor and the brand new one. Performance is the same as well.
I have replaced all the vacuum lines with the rebuild, so strongly doubt there is a vacuum leak (doing a leak test tonight). Belt is new and does not appear to be slipping. Problem cannot be Boost Actuator or Solenoid since as mentioned above we bypassed them and saw no change in performance (or in boost readings).
Is there any way to know if this really is likely the supercharger? Could the boost meter just be wrong, and the computer or some other componant be causing very substanial power and mpg losses without trouble codes or rough idle? I am stumped here.

I think you may be overlooking this. Have you taken the supercharger belt off to see if the motor runs alright without the blower?

I'm suspecting that with the longblock, you may be having belt slip causing you to run low on boost. Just a guess though...

Thanks for the suggestion!

I gave that a shot and performance appeared similar to before but without any boost at all. I also changed the fuel filter and did a fuel pressure test (which was in spec) since my last post.

I finally decided to pull the blower and take a closer look because it seems like it is all that is left to be broken at this point. Upon closer inspection it is in much worse condition then I had believed when it was installed on the new engine. There is very substatial wear in both the housing and the blades and I am now almost certain the low boost is just low boost from a shot supercharger. Ordered a rebuilt unit and will follow up if that fixes the problem.