Starting and Stopping- related?

[Choking Hazard]

My brake wear indicator has come on and the problem is NOT in the sensor or the wiring. The pad wear light glows dimly all the time when the ign is "on".  When I disconnected the sensors the light glowed brightly.  I'm convinced it is related to the starter replacement I recently had done. I'm thinking it is grounding through the starter motor or the solenoid or something.
Will it damage the alternator to disconnect it then turn the key? I think this HAS to be related to the starter replacement.  Also, my power windows will now only operate in "acc", not when the car is running....  This also began right after the starter replacement....
How is the starter wired?

[Choking Hazard]

Here is the explanation of the odd behavior I had after the starter was replaced...

http://www.m42club.com/forums/showthread.php?t=4679&highlight=windows
Its the wire going to the top (smallest) post on the solenoid.  I cant tell what color the wire is, but I tested with a 12 volt test lamp and determined that on MY starter that was just put in, the lower small post goes to the ignition switch.  When I turned the key to "start", if my light was connected from there to ground, the test light came on, but was off at "run".  More importantly, with the test light acting as a jumper, the windows worked and the "brake lining" light went off.So I'm going to wire a jumper in tommorow.