I’ve used ClownBD to get the order of the files straight and produce one m2ts file. It really isn’t hard to use once you get started.
I personally wouldn’t use SUPER for H264 conversion and compression to a smaller size. Though I have to admit I haven’t tried it in a while.
What output format do you want? .mkv or .mp4 perhaps? There are a number of different programs for this, including Ripbot 264, MeGUI, Handbrake, and even AviDemux.