I need a tool which can minify, optimize and munge many files of those possible types
My suggestion would be to put all of the JavaScrpt inside a in the header, and put all of the CSS in a
tag as well. Then optimize to the best of your ability and then minimize it on your own. No software will ever be able to handle every case. If you are trying to minimize the file size then just remove the newlines and non-necessary spaces.
I also found this, which should work on your file with all 3 in it.
Also be aware that if you start removing optional tags you could run into some problems. Some browsers don't cooperate as well as they are supposed to.