So as I mentioned before, initially when I got the car, the soft top refused to go up past 1/2 way. It would stop and you would hear a mechanical "click" It would go back down electrically. If you turned off the key, the top released hydraulic pressure and was then able to be raised manually. If you had the top sitting on the front latches, and then pressed the close button it would latch in the front and the rear section would fold down and latch electrically as well.
When trying to open the top, the rear section would fold up however the front latches would not release electrically. If you released the latches manually with a 6mm allen key, and then attempted to open the top electrically, the rear section would still come up, then you would have to turn off the key and manually fold the top back. Then turn the key back on and use the convertible top switch to close the top cover.
After doing some research into the issue, I came across a Mercedes Benz document for diagnosing the soft top. It stated that in the closing mode, the top not going past 90 degrees was caused by one of the two window down limit switches not closing. The car uses window down limit switches to determine that the windows are in the all the way down position. Only once the soft top controller has a signal from both doors that the windows are completely down does the soft top fold over the center section of the roof. Apparently the windows or the top can be damaged if the top moves with the windows up.
Armed with this information I tore into both doors (that was foolish of me as the wires can actually be tested at the soft top controller itself - more on that later). The window limit switches are clearly visible at the bottom of the door, almost in the center of the door. You will also see a little metal bar with a rubber cap on it attached to the center of the window regulator with a 10mm nut. This is designed to contact and close the window down limit switch when the window is all the way down in the door. Each window limit down switch has a plunger that can unclip from the mechanical switch. You will have to peel back the wiring loom with a razor blade to get to the actual wires. Each switch has two wires, a brown wire which is the wire that supplies ground to the switch, and a gray wire which leads back to the soft top controller.
The brown wires should show continuity to ground at all times, and the gray wire should show continuity to both ground and the brown wire when the switch is engaged. You may have to unclip a portion of the switch to be able to access the wire. In my particular case, the problem was the brown wire in the driver's door had somehow become disconnected from ground.
After tracing the wire back to its source I found it had been disconnected from the driver door and was not providing a ground source to the switch. After repairing that connection, I started the car, and hit the top close button and hoped for the best. And the top went up, I was waiting for the click but instead the roof folded over the seats, and voila it latched in the front. For some reason it seems like you have to let go of the button, and press it again for the rear section of the top to latch. The top opens fine as well, and all seems to be working now. Now onto upholstery repairs...
Here are some pics of the car with the soft top up.