Several members have the same problem. Some have resolved it by greasing the roof points:My top works all year , but not when it's over 90 degrees
1998 slk kompressor
This link has lots of good info.
The only comment about removing the boots completely is that this is a fair-weather solution; the boots are to stop the rainwater (and any other fluid like car-washing) getting into the switches.I took my headliner off and removed those clear rubber boots for the micro switches and my top is working perfect on hot days now, I ask my mercedes dealer about this and they had no idea. I called one in another city and they had a guy that had been there 30 years and he confirmed this should work....thanks guys!!!