Roland, I think I like your #2 approach better. If you lift one end of the top more than the other, you can put some serious strain on the plastic guides that ride on the tracks up the sides of the bottom half, which could break them.
If you lower the top onto 2x4s, you can then loosen the adjusting bolt on the appropriate cable to get even more slack, which should allow you to unscrew the cable under that window easily, then reconnect it easily when you are finished with the repair.
The only problem I'm seeing is if you have to work on the area where you have a 2x4 holding the top up. Possibly, you could support that part of the side very near the front corner, or, maybe with a 2x4 between the a-frame at the front and the top?
How are you planning to repair the rotted section? It's a load-bearing part of the top, so the repair needs to be "sound".
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