[Tiwaz]

Extract the part of the .pk3 file you want to edit, including the folder structure. Edit the .tik files in notepad, and save them. Compress the files and folders to a .zip and rename to user_huge_clipsize.pk3 or whatever, and put them in your MoHAA\main or MoHAA\mainta (for Spearhead) folder. Should work.
Only the files you have edited should be present in the .pk3, more files only will only use up space.

I use WinRAR for (de)compressing .pk3's, by the way.