It's difficult to suggest a definitive, specific tool to suggest how to combine the files, other than you need a sound or video editing program to match up the files with a video source. The source needs to be frame accurate for the DTS files to match up perfectly, which I know the broadcast versions aren't. For example, the TB releases are missing between 10-15 frames each which will mean these frames either need to be reinserted from other sources or the sound chopped (11 missing frames in TESB TB release are about 3 minutes into a reel!).
The best reference for accurate video sources are the numbers posted in the standards thread by Darth Mallwalker and msycamore. The reel changes are in the correct place for the start point ('Star Wars' appearing on frame 711, all numbers can be offset for different start-frame numbers). Having just finished my own synch of ROTJ, there is a few seconds of overlap at the start and end of each reel, and with some reels the waveforms for identical overlaps appearing different, with matching sample peaks and troughs appearing unrelated; as such, the reels don't match 100% sample for sample, end to end, but are close enough to be unnoticeable.
My method you know already and have published in the other threads, and I'm not sure there is an easier way. It's certainly not a case of "crop x amount from the beginning and end of each reel" as you would using an AviSynth script with video.
If you were to mux them to a DTS file, you would have to get your hands on the official DTS encoder. I don't think there is another application that can do it, and there certainly aren't any free ones due to licensing. With both the DTS and Dolby encoders you need the 6 mono wavs for each channel and assign them accordingly in the encoder. Then its often just a case of clicking 'start', unless you start messing with 2.0 down-mix matrices and such. The only free program I know of that works similar to the pro encoders is EncWAVtoAC3, which doesn't encode to DTS but is a user-friendly way of creating 5.1 AC3s.