Here's how that $1,000 deposit works. The dealer requests it as insurance that you will go through with the sale, subject to approval of financing. If financing falls through, there is no deal, and you get the deposit back. If financing does go through, you will get the $1,000 back. Most people apply it to the down payment. If you refuse delivery of the car, and there is nothing wrong with it, you forfeit the $1,000. By stopping payment on the check, you have, in effect, committed fraud, and if the dealer pushes it, you will indeed be visited by the police, who will give you a court summons. You will do your explaining to a judge, not to a cop. If I were the dealer, I would simply drop it and send you to see my most hated competitor.
FWIW, you don't really have to give the dealer a deposit. Last new car I bought was a Subaru in 1998. After I test drove the car we settled on a price, but no papers were signed, as I wanted to pursue my own financing, and let my wife try the car prior to final sale. He wanted a $1,000 deposit to "hold" the car for 14 days. I told him if he could sell the car before I made up my mind, to go for it. I'd simply buy another one from another dealer. I wound up buying the car and never gave him a deposit. Another time, a dealer wanted a $1,000 deposit, and I told him all I had with me was $100, and I didn't have my checkbook. He accepted the $100.
It appears to me you're not well versed in the ways of the world, as you keep compounding your mistakes. Stopping payment on that check was not the smart thing to do. Hopefully, ther dealer will see this as not worth the bother, and drop it. I really hope that's what happens. I'm guessing you are young. If I'm right, get an older friend or relative to go with you when you make a major purchase like a car. And for God's sake, don't go on the internet asking for advice from a bunch of strangers that don't know any more than you do.