There seem to be commercial DVDs available -- unless these are rare episodes or something -- so you really should use those as your source. Your AVI rips will have been resized, probably to different resolutions. To convert them to MPEG-2, you will have to resize them to make them DVD compliant and to make them match each other. This will involve learning a fair bit about resizing video and some of the basics of Avisynth. Once you have done that, you can encode with HC Encoder, which is a free high-quality MPEG-2 encoder, and take your files into Womble to edit, if you are determined to edit in Womble.

Working from the DVDs would be easier. Even then, editing in Womble is not as easy as it looks, if you want to do it properly. You have to learrn to work round its bugs.

Really, Womble is designed to edit and smart render MPEG-2 files. It isn't really very good at anything else.