Hi Kerry , I know this thread is old but it seemed to fit except for being for DVD.
I didn't have the programs you suggested installed on my Windows 7 but I did on Vista. So I downloaded the new versions & installed some of them.
MKVCleaver separated out the wanted tracks.
I wanted to see how the separated audio track worked in Audacity so I used it.
It took me changing a few settings in Audacity for it to get 6 channels "Exported" instead of one mono channel.
MKVMerge GUI was able to do the remux.
I don't have ClownBD because it requires JAVA (Which I don't have installed on any OS I have). Otherwise I would have it.
Before I checked back I had already been trying to figure it out with ffmpeg from command . This also worked & the final .mkv's are almost identical.
Here's the ffmpeg information for doing it in one step from the MakeMKV created .mkv with the HD-DTS MA audio.
Generic command set as many maps as you have or want subtitles.
At Command prompt cd to "\path_to_ffmpeg_here".
ffmpeg -i "drive_here:\path_to_MakeMKV.mkv" -map 0:0 -map 0:1 -map 0:2 -vcodec copy -acodec ac3 -ab "bitrate_here_remove_quotes"k -c:s copy "drive_here:\path_to_desired_directory_here\desired_file_name_here.mkv"
My actual command was this:
ffmpeg -i H:\MakeMKV\DESPICABLE_ME\Despicable_Me_t02.mkv -map 0:0 -map 0:1 -map 0:2 -vcodec copy -acodec ac3 -ab 640k -c:s copy C:\Users\Username\Desktop\MYT\7.mkv