ltrain

I have a 2000 saturn sl1 that I just had the altenator replaced at a local shop. When he first started it up the car was shaking and then he shut it off turned it back on and the car was idling fine. Now when I drive it the auto tranny shifts hard through gears and in reverse I have no power I have to give it more gas to make it go. I drive the car normal its not like I am beating on it and it shifts hard. The car has never been beat on. That's my first problem now another problem I have which started a few months before I changed the altenator is I get check engine lights for misfire #3 and small evap leak. It goes on for maybe two days then goes off. It does not stay on constantly. I changed the plugs and wires same problem. Any help for either of these problems I appreciate.