Success, finally. Using TMPGEnc (thanks Chef), I took the raw .mpg, edited it in the program, and encoded it within the same program. Only bugbears are that I encoded to DivX instead of XviD (although it does have custom option for XviD, which I am yet to try), and that it took WAY longer than expected (2 1/2 hours for a 1 hour tv show, 2 pass encoding, compared to less than 1 hour for AutoGK), but at this point, I am beyond caring about these tiny quirks, and I am yet to toy with the settings to try and improve them.
I didn't get a chance to try the TS methods, as I hadn't yet captured any shows in TS, and I already had a backlog of .mpg's sitting on my hard drive.
Thanks for all your help everyone.
Also a question, am I supposed to be cutting only at keyframes, or will any frame do?