Transmission

I have a 2000 hyundai accent I let sit for about 3 weeks to get a brakelight part and when I did I drove it to work the next day which is 12 miles and when I got about two thirds of the way I felt almost like a missbut on the way home it started again but got be like going in and out of gear so I replaced filter and fluid and running 55 for about five miles it started again and kept getting worse
is there some kind of controler that could be causing this also I live on a acre with alot of open land around me with all kind of critters (I looked at wire and did not see any problem)
I have owned this car since new and never had anything like this