I converted my Hyundai from Auto to Manual..have questions

So I just finished converting my 2002 Hyundai Accent (2 door, 1.6 engine) from automatic to manual trasnmission.  Everything works finr except the Check engine light turns on and it won't pass smog because of it.  The guy said all I had to do was take the computer from the manual I got the trasnmission and replace the one on my car, I did that and it didn't work....Any ideas?

find out what the code is then we'll take it from there. when you did the swap did you change the harness also?