About Extracting & Replacing files in a Custom ROM Custom ROM's come in as a .zip file. Is it good to extract those and add a few apps like Settings.apk(replacing), MMS.apk (replacing) with the existing one? Doing so and after that compressing it back to a .zip file would work when i try to flash it or not?
Replacing will probably work. However adding or removing files might not, Flashable Zip's need to contain a script which tells them what to do (in this case: installing, moving, copying files) You need to change these scripts to your desire, I don't know much abou that but XDA-Developers has a lot information about it.

Another Problem might be some sort of checksum which verifies integrity. You can make a Nandroid-Backup and test it yourself ;)