[Tiwaz]

Extract the part of the .pk3 file you want to edit, including the folder structure, or create the structure and files yourself. Edit or replace the files (use a tutorial for this) you want to change, and save them. Compress the files and folders to a .zip and rename to user_nice_grenade.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.

If this doesn't work, you have done something wrong. Most likely it has something to do with your .tga (size, compression, whatever).