Alarm it and Club it.
Also, I'd check to see if you had the car serviced recently at oil-change places or wherever you dropped the car off, it could be that easy to make a copy of the keys.
It's good to hear that Metro is finally running DNA from shirts and what not found from your car.
If they have a record in town chances are they will be able to match it.
I hate the way they don't do it for every incidence because of the amount of man-power/time/money that has to be spent. But once in a while if they do this, they can hold a record for each case and be able to catch 1 or 2 of the suspects so they can't go out and do it again.
Lastly, I am so surprised at the way people would even consider stealing the car. Is it not stock? It doesn't have super big wheels right? I'm betting that they seen your yellow-car and suspect that your father's car has similar parts in it.
I say, club it and alarm it and knowing you have the know-how to do it, also add a kill-switch to the car. Anything to slow them down will hopefully deter them from even attempting to steal it.
Glad you were able to get it back though!