Test your two vac solenoids on a 2 bolt braket on top of your intake manifold near pass side, it sounds like either one of your VICS, and VTCS is not in the correct position, these solenoids do NOT pull a cel on the msp, only when unplugged.
You can also run a 12 volt power supply to them and see if you can blow air through the ports (the side with 2 connections) the other side is the atmosphere reference and should not be clogged either ( there is a small box cap over these it has a small pinhole in it)
The VICS solenoid and vac lines is the one closer the the drivers side, and the VTCS is closer to the pass side, unplug these vac lines, run the VICS to a main vac/ boost line and unplug the vac line for the VTCS, the VTCS should have no vaccum when the car is warmed up, you can even unplug it at the check valve.
The VICS has vacuum at idle and up to the RPM switch point, when you start the car at any temp you should see the rod move with the actuator, if this is working incorrectly you will have horrible low end torque , and it will hesitate like crazy especially when cold, cause a somewhat stumblly idle, from running too rich and not using the right intake runners, this could cause the EGR to become very clogged too.
You can test these vac solenoid by using an ohmmeter and measure the resistance on the leads on the solenoid if it > 60 Ohms it is bad, anything over 1 megaohm throw it away and buy a new one.
Note: Some people on probe talk have had luck with temporarily applying 24 volts to jump the problems in the solenoid coil, but many fixed ones have failed months after fixing anyway, they are 100.00 to buy online, or you could goto a junkyard.
Also make sure your VTCS, is in its default position at operating temp (no vacuum to this actuator)
Also, the constant vacuum accumulator that the leads of these solenoids goto, sometimes gets clogged or the check valve gets weak, and cannot pull vaccum on both items.
I would take the vac line off of the VTCS, the only one with check valve on that side.
And then run a single vac line from this vac reserve nipple to verified working solenoid and hook it up to your VICS(torque/high hp) runner actuator.
I would then make sure with your (cold start butterflies / the one w/ check valve) is unplugged from the vac system and use a screwdriver to push the lever closest to the Intake manifold gasket to make sure it is free to move and the spring returns it after you push on it.
This pic shows the VICS actuator freely moving when off, and you should not be able to move it easily when the car is running.
Also shown is the VTCS check valve to the left that can get stuck also.
This makes sense you have no low end torque, and are limited by the runner restrictions from the closed VTCS actuator,
I tried driving my warmed up car emulating this problem, i also could not get above 4500 RPM and made 2 psi of boost, put it back the way it should and bam 10 psi and pulls like a champ.
I have a feeling this is your problem, hope this helps.
