I never had a chance to drive my donor, it was wrecked when I bought it and had broken 1 CV axle so it had no drive possibility. If you've already gone past some of these things just ignore them, I'm not sure how much you've looked over your donor exactly.
The smell of burnt rubber: is your parking brake sticking on 1 or both sides? Not if the handle is released, check by jacking up the rear axle and spinning the wheels by hand with the parking brake handle released. This could be a power drain and smell source.
The lines you now have in place match what I have on my 06 SS/SC, but are there any intake leaks? Does the brake pedal sink after starting up or does it stay rock hard like it would be when the car is off. I would think you could spray a light soap solution near any connections on the intake to look for bubbles, or make up a smoke machine (I think Ross and I have each made one for cheap, I can find a link if you need).
Seems very odd the previous owner removed the electronic boost gauge and went to a plumbed version, stock would top out at 12psi and I would hope the wires would still be present but I would guess the car didn't come with the original boost gauge, it was physically removed for the aftermarket one?
If it was clutch slip then you'd see the rpm's jump without direct connection to speed, I think this is the easiest since you can see this on the dash. I think the easiest test for clutch slip is to put it in higher gear at a lower speed and give it a good amount of throttle. I think I have that correct, I've never actually had clutches wear out on my cars so I can't verify.
Given that the car is a new purchase, how's the air filter? The supercharger might be fighting a badly clogged filter and causing a power decrease. Since it's in the front fender space it may have been neglected before.
Sure, the cobalt isn't as light as the goblin, but I do know you can still really feel the power of the SS/SC nicely throughout the rpm range. It should feel like a very solid torque curve throughout, just not quite as much acceleration as you'll get when it's in the goblin frame.