HELP! 03' focus sputtering

Hello! I have a problem with my 2003 Ford Focus ZTS and am all out of ideas. It has a 2.0L ZETEC engine and is automatic. I recently replaced the Starter, Alternator, and battery cable because the car was having some current issues. All parts are brand new, non-refurbished. The car cranks fine but is now sputtering. When I drive it, it seems like it has a hard time switching out of first gear and and will hit 3-3500 RPM before the gear shifts. I am $500 deep in this project and now I am not sure as to which direction to go.

First, take it to an auto parts chain store and have the codes read. Post them here in P0123 format. If the engine is “sputtering” there should be some stored code(s) to read.