About batch muxing. After searching online I found https://www.youtube.com/watch?v=3LCnU4aT-yM to be a good tutorial on using command line for mkvtoolnix to do batches.

Below is batch command I used to mux the mks to mkv for all episodes. For this one, put the all the mkv and mks in the same folder and keep each mkv and respective mks same name.
Copy the below content on notepad and save it with bat extension in the working folder, and run it.

set mkvmerge="C:/Program Files/MKVToolNix\mkvmerge.exe"
set output_folder=H:\OP
for /r %%a in (*.mkv) do call %mkvmerge% -o "%output_folder%\%%~na.mkv" --language 0:jpn --default-track 0:yes --language 1:jpn --default-track 1:yes "%%a" --language 0:eng --default-track 0:yes "%%~na.mks" --track-order 0:0,0:1,1:0