After I removed the hard top to open a soft top, I discovered 2 problems.
1) The soft top wouldn't close ate the windshield and the rear portion of the soft top wouldn't go down at all
2) After I took off the soft top completely, and put back the hard top, the red light stays on and starts beeping, once I start driving.
Please advise what to do, what the problem can be.
Thank you

Did you try pulling down on the soft top to get it to latch to the top of the windshield? There is an indention on the top just above the rear view mirror so one can grab hold and pull down. The soft top does not always automatically lock in place at the windshield.....my mom's 91 300SL never has, we always have to pull down on it....(with considerable effort). Considered normal according to MB.

Once the front of the top is latched, the rear should go down and latch automatically.

Your hard top problem is most likely the car telling you that the hardtop is not seated properly....remove & try again.
We usually have to fool around with the hard top a couple times when changing tops on the 300SL.

I forgot to mention... while pulling down on the top, you must have the open/close switch engaged with your other hand to keep the open/close cycle in process.

__________________
73 220D
08 997 C2S
03 Jetta wagon TDi

There is a sensor in the middle and the magnet is located on the soft top. I simply replaced a sensor and it works now. I still have problems with a hard top. Seems like 1 side doesn't get pulled down by hydrolics fully.
Steven