I just completed about 120 handsaws for two of the regional tech
schools.
I used to machine file them but it made a nicely uniform mediocre job
at best.
What you want to do is always file in the direction the tooth is set so
that the file cuts evenly without chatter.
This includes rip saws as well so that you even out any angle errors
and the saw cuts true.

Don't go balistic when you joint the teeth- take a swipe across the
tops and then file a stroke through the teeth and see how you do.

Try to limit your set to the top 1/3 or so of the tooth, go easy
because you can add more set but getting rid of too much is not so
easy.