I then explained to her what has happened since I wrote my email. I told her how I can't prove that the key for the security system was there or not, and have no basis on which to accuse them of losing it, but that the coincidence of a piece going missing from my steering column right after I had my steering column dismantled is hard to ignore. I said I felt as though I paid $98 to have something broken, $98 for them to figure out what that was, and another $92 for them to fix it. She agreed that it's suspect, and promised to refund $190 (I'd like all $388, but we're getting somewhere).
She said that people are often surprised at how long body work takes, and I didn't argue that. I told her about how the gas pedal has been misplaced, and since they had the car a whole month, the job should have been done completely. Given the charges I've had to take on for getting the flasher broken, I didn't want to take the car back to the body shop only to have to pay them to figure out what they should have done and then pay them again to fix what they should have finshed in the first place. She said she'll talk to the body shop manager and I'll be getting a call from him today to discuss what needs to get done.
So it seems like I'm getting somewhere. I'll post again after I hear from the body shop guy. Thanks to all of you for your encouragement, especially in regard to sending the email. My grandmother always told me if you want results you have to write letters. Time and time again, she's right.