I removed as much paint from my frame as I could but there's still paint left on there. Can I use Metal Prep on it?

No, it is not recommended to use Metal Prep on paint. Use a wire wheel or grinder to remove as much paint as you can, and only use Metal Prep if you can completely get it down to bare metal. If not, scuff up any leftover paint and proceed with two coats of rust sealer and one coat of AG111, Chassis Black Finish, or your own topcoat. It should encapsulate the leftover paint just fine. However, if you have large areas of bare metal after removing the paint, you can spot treat them with Metal Prep. Just wash off any paint with water that may come in contact with Metal Prep.