As long as they provided a rental until the check is cut, you probably wont get loss of use because they gave you a car to use. As for value of aftermarket parts, you may be able to get them to cover the damaged parts, i.e. fender flares, wheel(s). Any other parts that werent damaged they arent going to cover since you will be keeping the car/parts. If you were to surrender the vehicle to them, you could remove the parts but it sounds like he really wants to keep the car (I would too).

As of now, it looks like, value of vehicle with rebuilt title $1100 - buyback value (shouldnt be anymore than $200) plus whatever you can talk them into covering (flares, wheels, etc). Or you can sue for whatever you want....

Its a really shitty situation, but when your dealing with a ~15 year old vehicle with aftermarket parts, its an uphill battle. Rebuilt title makes it even worse. Thats why classic/muscle cars have stated value insurance, because the older the car the lower the KBB/NADA value, and even less for common insurance values.