Did a car stereo install in my 1997 Ford F-250.

The stereo and new speaker front and rear install went well. I wanted to add sound deadening to the door. I pulled right front door panel added sound deadening material put the panel back on everything was ok. Drove truck to job site next day got home no problems. Pulled left rear panel and did the same sound deadening process as before, pulled the drivers door panel same process. I put the panels back on and drove truck to Auto zone for a couple parts and on the way noticed the tranny wasn't shifting properly the overdrive light was flashing. In addition the speedo wasn't lite up. Back at the house I found that the interior lights not working along with door locks. When pressing door unlock button the marker lights flash. I assumed that a ran a screw through a wire causing a short. I've removed all the door panels and speakers which didn't solve problem.