Back in the days of the anime fansub era, timing subtitles was a job well known
to be easy, but annoying. The best way to avoid burn out is to do it fast. For
this purpose, very convenient subtitling software has been built. You can use
these tools today when subtitling YouTube videos. I'll give a quick
introduction in the following.

First download the video with youtube-dl. Getting a low resolution version in a
compatible format is best. You can type this in a terminal in the folder where
you have youtube-dl.exe or copy it in a batch file:
youtube-dl -f 18 https://www.youtube.com/watch?v=4q0X_Y9s77Y

Open the video from the "Video" menu and from the "Audio" menu use "Open from
video" to load the audio track.

For timing by audio, I recommend you watch these two tutorial videos made by
The Fluff. Using the automatic timing post-processor is also introduced in the
first video.

http://mod16.org/aegisub/timingtutorialimprovisation.mkv
http://mod16.org/aegisub/timing-fullspeed.mkv

Done like this, with a bit of practice timing by audio shouldn't take you much
longer than the length of the video in realtime or can even be faster if there
are many pauses.

If the video already has some lines hardsubbed in Japanese, you will want to
make sure that your subtitles start and end on the exact same frames as those
subtitles, even if it doesn't perfectly match the audio. Otherwise it will be
perceived as annoying flickering. To do this, select your subtitle line,
(right) click on the time slider below the video and use the arrow keys to move
through the video. When you have found the first frame where the Japanese
subtitle appears, press Ctrl+3 to set the starting time. Find the end frame and
press Ctrl+4 to set the time. After setting each time, use the cursor keys to
confirm that the subtitle appears and disappears as desired. Sometimes setting
the times like this is a little off. In this case, manually adding or
subtracting 0.01 second usually fixes things.

Once everything is done, use the Export function to export your subtitle file
to SRT format. This format can then be simply uploaded to Youtube. The exporter
will take care of everything, such as overlapping lines. Long lines will be
automatically wrapped by Youtube's UI. However, since the wrapping might be
done in an ugly way, for long lines it makes sense to manually include line
wraps using \N to make everything look balanced.

Downloads:
youtube-dl: https://rg3.github.io/youtube-dl/
Aegisub: http://www.aegisub.org/downloads/