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Congrats on getting the Boxster! this is a pretty common issue. I personally fiddled with the top for months and tried many different things until i figured it out. I did learn a lot in the process though. I have a 2000 like you and because the light stays on and the top gets stuck in the open or closed position i think it's one of the gears failing. Basically what happens is the nylon gears inside the transmission get brittle with time and crack so although the electric motor is pulling, the top wont move. When one side moves and the other doesnt the top goes out of alignment and it's never fully open or closed. That's why the light stays on sometimes, because it's not fully in one position or the other.
You can eigher get a pair of transmission for both sides (you can find them used for not too much money) or get the transmissions out and check which one is cracked inside so you only buy the one you need. Make sure you get the right year, not all are the same. Ours has a position sensor inside the transmission on the right side of the car (if memory serves), newer model transmissions dont have the sensor inside, it's somewhere on the chassis. Do some research to learn what year the design changed if you cant find one for the year 2000 exactly.
It's not hard to replace the transmissions, you can get it done with some basic tools. if you need to move your top manully, check your owner's manual, there is a process to disconnect it.
Once you replace the transmissions you have to realign the top, otherwise it still wont open or close fully. There's plenty of info on how to do that, it's not difficult.
Good luck with it!
Cheers,
Cristian
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