The one in the file contains the stereo audio while the other flac audio is 5.1 if you want that instead.

The easiest method is to download the program hjsplit @ http://www.hjsplit.org/
Choose the proper version you need near the bottom of the page.
Download it, (extract it if you have the windows one).
Run hjsplit.exe
Once the program opens, you should have 6 options.
Choose Join
Now a new pop-up windows open.
Click on Input file
Go to the proper file destination (such as your downloads folder, if you're not already there)
Now there should only be one file to choose from (or other folders)
Named [fansub]The Garden of Words -kotonohanoniwa- (1920x1080_x264Hi10P_flac_3subs).mkv.001 or similar file ending in .mkv.001
Click Open.
Now the pop-up menu should display the input file and the output file(and you will see that it ends with .mkv not .mkv.001 or anything)
Now all you have to do is click start.
Once it finishes (and tells you), you should have the complete file. Huzzah!
Now you can play the video.

If that doesn't come clear, here is a youtube clip: http://www.youtube.com/watch?v=CrCurzfT4IM

Another program that will get the job done is filejoiner @ http://www.igorware.com/file-joiner
This will feature similar steps.

Lastly there is another options, if you're up to the task.
open up the command prompt (win+R then type cmd.exe)
move to the directory containing the split files (use cd) - or move the files to the user root folder.
then type
COPY /B <source file1>+<source file2>+<source file3>+.... <destination file>
where <source file1> is .mkv.001  and <source file2> is .002 and so on. and <destination file> is the file ending in .mkv.
This is easier done if you rename the parts before hand to avoid unnecessarily typing/mistakes. do A.mkv.001 B.mkv.002 ....

After executing the command windows should give you the complete file with no issues during opening/playback.

For linux:

cat file1 file2 > file3

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The link still works and it was only uploaded yesterday.

I have vlc 2.0.6 and it plays fine, except I have to manually change to English subtitles from the Japanese default.  So at least you can work from the assumption that it can be done.

It's hard to say what may be the problem.  Probably your download was corrupted somehow and you may need to try again.  If so, you might also consider getting one of the other versions such as Commie's, Coalgirls, or WhyNot.  This particular version may also be lacking an English translation of a few lines at the end.

Another thing to try is to re-install vlc.  Occasionally, some part of a program can get screwed up.

Either way, there's some really beautiful animated scenes of nature and a nice story to make your extra efforts worthwhile.

btw, I assume from your note that currently this file doesn't play at all for you.  If there is some more specific problem (audio missing, video glitches, etc.) that may suggest specific problems.

And just to mention it, there are two files here: the 2GB mkv is the movie.  The 700MB file ending in "flac" is only a supplemental soundtrack, not a smaller version of the movie.  It can't be played by itself.  I don't expect that's the problem, but I thought I should mention it.  Good luck.