Ripping to mp4 with multiple audio tracks and optional subtitles

[Super Chris]

So I've been ripping my blu-ray collection using the tutorial here:
http://gizmodo.com/5161848/how-to-rip-blu+ray-discs
and I have so far been very happy with my results. However, there are a handful of discs where I need the finished file to include multiple audio tracks and optional subtitles. After futzing around with RipBot I am not seeing a way to include more than one audio track, and the only subtitle options I'm seeing are to hard-code them.

I am ripping my collection to mp4/m4v, and with handbrake I have had no difficulty including multiple audio/subtitle tracks on the DVDs I've ripped. So now I'm wondering how I can do it with blu-ray. Once I rip a disc to my hard drive using AnyDVD HD is handbrake able to encode it? Would handbrake be able to identify the playlist files, since some movies are broken into multiple video files? Or is there some other process I would have to follow?

Also, as a lesser question, is there a way to chop off the last couple seconds of an mp4 file and then splice two of them together? It would be nice to combine my Lord of the Rings trilogy from 6 files to 3.

[hello_hello]

I rip Bluray discs using AnyDVD and HD Streams Extractor. The former sitting in the background, the latter extracting the video and audio streams etc. HD Stream Extractor is a GUI for eac3to. Or alternatively there's Clown BD.

The main reason I use HD Streams Extractor is it's integrated into the conversion program I use, which is MeGUI, but it should extract the video to an MKV file and save the audio streams to your hard drive.
In my case I use MeGUI to encode the video, then tell it to add the extracted audio to the video when it's done. Or it'll convert the audio before adding it etc. I've no idea if Handbrake or Ripbot and add external audio or if the audio must be contained in the file you're converting.

If not.... you could use Handbrake or Ripbot to convert the video, then add the audio manually. I'm an MKV kind of guy myself.... so I'm not overly familiar with working with MP4s, however for manually adding existing streams to MKV files there's MKVMergeGUI, for MP4s My MP4Box GUI should do the job, I assume.

[hello_hello]

PS Both MKVMergeGUI and MP4 box can split files, so you could split off the last few seconds of each LOTR file, then joing the two large remaining pieces together. You can only split on keyframes, so you mightn't be able to split in the exact spot you'd like, and both files have to contain the same type of video and audio.