I am trying to munge my side but when I run the game it crashes, saying it doesn't have the mission/lvl. I reread the document and it says when you munge it a file called (you 3 letter side).lvl should be in the _LVL_PC folder in map.data. I check and it isn't there. when I try to munge the side I read it can't find the req files. what should i do?

is it a custom side?

yes it is

you could try munging your side in another map then copying the lvl file into your LVL_PC folder...
You might have set up the req files wrongly.

I munged everything and it says in errors levelpack shell.req: Input file shell.req does not exist.

do a clean, or a manual clean (see the FAQ on how to do it)
Then remunge with only common checked.

As a point of information unless you are creating new sounds or a new shell or new localization you do not need to have those checked. As well after the first munge you don't even need to have common checked unless you have changed your scripts. Makes the munge go a lot faster.

Have you successfully gotten a blank map to work (without custom sides)?

I can't get a blank map with just common munged to work.

How long does your munge take?