First off, there is only 1 motor for the Boxster top and clam shell. Not sure what you mean when you say one of the motors failed. My guess is you had an issue with a top transmission on one side so now the sides are slightly out of sync.
You need to access the motor and remove the drive cables. Use a cordless drill to spin each cable until you have the two sides evened out. It's a little trial and error but really not that tough to do.
Nothing is hard to access so just have to do it.
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