The motors and board are still available from Lionel - so, the replacement motor should be the correct one. I assume you were replacing the rear motor.
Is this what you purchased and /or received?
Have you tried an engine reset?
When you test the motors - check the rotation - are both motors jerking? perhaps the color code isn't the same polarity on the replacement motor and they are opposing one another.
A photo of the board would help - a bulging cap may indicate another problem. Here's the replacement part photo - the creases in the top are for bulging safety when they begin to fail