will a 2001 motor work with a 99 tranny?

Hello, If the engine and transmission are identical from both vehicles, there should not be an issue. If the donor vehicle had a newer version of that transmission, there is likely to be issues with running the issues with the existing powertrain control module (PCM). Also, if the powertrain or engine control module was brought from the other vehicle, you face anti-theft system issues where the new module is not programmed for the VIN number of the vehicle.