A Turbo Bypass/Blow Off Valve and the one in the M62 Supercharger are for totally different things.
If you don't have it connected then the only gain you will see is a VERY mild increase in boost pressure earlier than before, but it's totally a function of delay from the vac system closing the valve.
Where you wont see any gains and in fact see a loss is in MPG ratings. The S/C goes into bypass so that it equalizes the pressure on both the atmosphere and charge side of the rotors. When the the valve is open it only takes like 3 HP to drive the S/C vs. about 25-30 when it's closed. For cruising you don't care about power and the difference would be like driving around with the A/C on, but for acceleration it's closed anyhow and from 4000 RPM(engine) on you'll be using 25-30 HP to spin it.
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Now where this whole idea of limited boost comes in is that something is preventing the supercharger from seeing a boost pressure that we mechanically expect based on rotor RPM.
The initial thought was that maybe the PCM can act as a wastegate controler and crack the bypass open at higher engine speeds to limit overall manifold pressure. If that was the case then by disconnecting the vac line to the bypass valve even a butt dyno would probably puck up the increase in vehicle performance. (Also anyone with a boost gauge would see the higher psi too)
Since that doesn't seem to be the case (Has anyone verified that) Then something else could be causing the flow restriction that can open and close to limit air flow to the engine. The other possibility would and could be the electronic throttle control. Remember Fuel delivery and ignition timing defines engine RPM NOT the throttle position. It's possible that the PCM could be closing the throttle plate to prevent no more than a specific volume of air to enter the engine and preventing more power from being made.
This may be both a limit of the Mass Air Flow sensor used and MAP sensors.
I'd track down this issue in 2 possible ways.
1. Find a Saturn Tech Friend with a TECH2 do do a ride along in your REDLINE. Monitor the throttle position and/or motor voltage to see if it drops off near redline.
2. Hook up a FLUKE Multimeter to the voltage input line of the throttle motor (including a resistor to hide the multimeter from the PCM) and see what the signal reads through a redline run.
You may be amazed at what you see. Try to record a shift and see what the throttle position does under that condition.. <- Emissions causes that..
This is just the beginning of resolving the lost boost...
Just keepting the throttle plate open 100% to redline may not be the answer, it may also max out the MAF and set a DTC or even worse limp mode. <- speculation 100%