Sorry to take so long to answer..

Still have problem, But advised by my friend who was a master mechanic for Mercedes Benz for 5 years and his specialty was the SL model.
The procedure varies by year model.
If it is 96 or newer everything seems to be tied to the window memory.
The system learns specific sequences of events.
Disconnect the neg terminal and wait minimum of 15 minutes.
Reconnect ( you will loose the radio and will require your code).
Start the car and run the window up or down but start from the full open or full closed position.
If all the way up run all the way down and release for one second than press again and wait 10 seconds. You will hear the window go through some minor changes and slight movements. once released run the window to the opposing position, up if you were down or down if you were up.
once up, release for one second and hold for 10 seconds. repeat process with the other window. To validate you have done it correctly push the window down switch and let the window come down automatically. If the window automatic down does not work you will have to repeat the learning process until the automatic function works for both windows.
The top, and roll bar are dependent on the windows knowing what to do.
Everything should work after these procedures are followed.
This has worked to a degree for me but I am waiting on new info from my friend in Belgium. Will update when new info is available.