No idea where it went. I can't find Franklin's car anywhere on the map. I think I remember getting an SMS in-game that said something about his car being towed or stolen or something. Where can I get it back? I just saw the car's icon again on the map and went there but it was police station and I paid $250 to retrieve a car that isn't original Franklin's car. It's kind of crappier.
This is a known issue with the game. Cars that have been stored in a single-player character's garage are notorious for just disappearing without a trace. Unfortunately, until this is addressed with a patch, the best advice is to not spend money on modifying cars in single-player mode.