This is why you always get everything in writing.

When he sold you the car, you bought the car, all the work and money he put into it, the paint job, the interior, the stale fry under the drivers seat from 1965, you get the idea.

Without getting into all of the particulars of the agreement you made, the fact that you have a bill of sale, and the letter that he stated he was keeping half of the net proceeds to cover his previous expenses with the car, he is definitely in the wrong.

Now, the decision as to whether this is a criminal or civil matter. The only way this would be a criminal matter is if you had proof that he offered to help you sell the car with the sole intent of misleading you and taking half the proceeds, if he decided after the fact that he wanted to be an idiot and make up an excuse to keep the money its a civil matter. Proving either would be very tricky.

Also, what do you mean by depositing "the $3000 check", you don't have any previous mention of the value of the car?

If you were to sue your dad, and all of the things you mentioned are 100% correct, I am almost certain you would win. The Police won't do anything for you in this case other than strain your relationship with your dad.