2001 Honda Civic Car has random transmission issues

Hi, I have just recently started having transmission issues(about 3 days), but they come at random times. I first received the problem when I was trying to get my car out of snow. I was putting my car in reverse and drive to let it free. I made sure I gave my car appropriate time and did not aggressively use the gas. After the check engine light came on and I could smells something burn. Now the check engine light will come on every time my car starts to have problems, but after the problem goes away the light switches off again. The problem I have is the car randomly has trouble going from second to third gear and I believe there is slightly a hard push from gear to gear. I believe the problem happens after longer periods of driving. Most of the time it shift correctly, but randomly it have issues. My only thought is it could be a sensor. Any help would be greatly appreciated. Thank you.