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Just guessing, sounds like one of the micro switches is bad. A couple others here have reported tops that only went half way were caused by a bad switch on the #3 top bow that tells the computer the "state" of the top position.
Edit: Just remembered as I thought about this, one person mentioned that there is some kind of "actuating arm" that attaches to this micro switch on the #3 top bow. That arm fell off and as I recall the new switch didn't come with a new arm and it may not be serviced as a separate part by GM. So maybe only a missing "arm" is the problem, not necessarily the switch.