My car recently wouldnt start, I had friends n.

My car recently wouldnt start, I had friends n neighbors look at it and tested starter, battery and ignition switch and he said all were good and there was some sort of problem between the ignition switch to the starter so I took it 2 a mechanic, they ended up telling me it was the starter and also got me to pay to get a new back brake caliper and the master cylinder, the brakes I have to pump 2 get to work now, but my problem is when I got the car back the alarm and radio no longer work? I have a friend who is telling me some short in the alarm probably kept it from starting and the mechanic more than likely cut a wire or something to the alarm. Could I get any input?And could you tell me what the relays are on the car above the fuses, because I went to pick a part place and took them all off another car like mine n I have 2 extra but 4 empty holes? Ita a 97 vw jetta vr6 2.8 thank you