I have this question with an open bounty. In summary, I couldn't get my phone to connect to the computer with a USB cable.I tried multiple things to solve the problem: including advice taken from superuser.com, XDA-developers forums and settings I experimented with. Though it's working now, I can't be certain which action or series of actions solved the problem. I cannot recreate the initial environment.
In general, for problem X I took steps A, B, C and am unsure if step C solved it, or any combination of A,B,C solved it. One of the steps was from an answer given on superuser.
How should I accept an answer and award the bonus? I would also like to document the steps I took in hopes of helping someone with a similar problem. For this I was thinking of answering my own question and explaining I'm not sure which combination of steps is the actual solution. Is this a good idea?
The problem was unusually complex as it was not clear if the source was the phone, computer or both. Furthermore the OS on the phone (Cyanogenmod) only has nightly builds and is not fully stable.