If you don't feel up to reading further, the bottom line is that I have a spare supercharger that I can offer you. However, as alluded to in  I certainly wouldn't put it on my own car because I can't vouch for its condition. It appears to spin freely, but I've already  on that subject!

Let's summarize your findings:

1. You have a 2002 C32 (what is your mileage?)
2. Your supercharger disengaged.
3. Your car goes into 'limp' mode. This is NOT always normal for supercharger disengagement and can equally suggest a completely different problem.
4. You changed your intercooler pump, but the problems still arise and you have 8 error codes.
5. You supplied power to the supercharger and it works (albeit intermittently).
6. You have an MB tech detect 4 errors pertaining to the clutch and supercharger.

Your error codes suggest anomalies in the following systems:
A) MAP sensor (B28)
B) Air temp sensor (B17/8)
C) Supercharger clutch (Y2/1)
D) Secondary air injection pump (M33)
E) Intercooler pump (M44)
F) Other evaporative emission control components
G) Oxygen sensors / catalytic converter sensors.

I think you have a more significant problem at hand and it is rather 'convenient' that the MB tech diagnosed the problem as a FUBAR supercharger (+ clutch) to the tune of $6,000.
Is it plausible that the MB Tech is correct and your supercharger and magnetic clutch are bad and this led to all the other codes?

There's no doubt that you have tested some of the components that may be in play; however, I suspect the proper diagnosis may require a more empirical approach. Analyzing codes and problems at one time point is useful. Analyzing codes and problems over multiple time points is more useful!

Before you commit to forking out for the parts and labor to fix these issues, I would go through each system with a fine toothed comb.

I would argue that the scope of the error codes that are being detected is too broad for it to be solely a supercharger issue.

Let me make my case for exhausting all other avenues first:

1. Our ME-SFI system is rather complex and has a wide variety of input and output signals. Many signals are interdependent on others; however, some appear to act/function autonomously.
See the diagram below for an overview of ME-SFI input and output signals.

One thing that upsets the ME-SFI is fluctuations in voltage.
Have you checked your battery to make sure there aren't subtle variations in voltage across circuits? Are you sure your harness is fine?
Another issue could be the presence of an aftermarket tune on your ECU.
You purchased the car used. Although you can't see any aftermarket hardware on there (except for filters), is it possible that the car had an aggressive tune with lots of hardware? If the hardware is now removed, you could still have the tune and subsequent problems. Who did you purchase the car from? You REALLY need to ascertain whether the car was heavily modified (or not).

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2. Analyze the systems that initially triggered the error codes. Let's start with the air intake temperature sensor (B17/8). Implausible readings from that will obviously lead to supercharger engagement issues. See the composite diagram below of B17/8. It's proper function is critical. Check the fine wire on the sensor to make sure it wasn't damaged (especially when it was cleaned). You said you are getting readings from it from a scanner so it probably is working. You never know though!

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3. Analyze the MAP sensor (B28: boost). Again, implausible voltage readings from this going to the ME-SFI will cause issues in supercharger engagement. See diagram below for how B28 interfaces with the ME-SFI.

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4. Check your secondary air system components. I am going through these issues right now and I'll write more on the subject at a later date.
Is your secondary air injection pump (M33) functional? It wont prevent supercharger engagement, but you should check it out anyway. Make a note to check the relay and fuse associated with M33. See the diagram below for the location and identification of the relevant relay and fuse.

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5. Importantly, your charge air coolant system needs to be investigated further. You changed the intercooler pump (M44) for the Ford Lightning unit and you know the pump works. However, are you sure that the coolant system is properly bled? There are multiple references to bleeding the system on the W203 and W211 AMG forums. Finally, check the fuse for M44. See diagram below for the location of the fuse and check out the relay listed also.

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6. (And finally!) Check the supercharger engagement issues separately. Before you fork out mucho $$$$ for a replacement supercharger, you should test the hypothesis that the clutch (Y2/1) is the culprit. See the diagram below for how the clutch and supercharger integrate. Remove the clutch and replace it with a suitable replacement that you know is functional. If everything else alluded to above is deemed operative (as well as the clutch) and you still don't get supercharger engagement, then yes - you have arrived at the conclusion that your supercharger is dysfunctional.

Click the image to open in full size.