You've really asked a bunch of questions here - how do i mod, how do i work with pak files, whats in the pak files, how do i edit the weapons, etc.
This is a tall order, but fortunately, the answer is easily available. Just go to the guides section on this sites main page (it listed on the left of the screen), and read the modding guide.
open pak6.pk3 with winzip and look for the weapon you want (bazooka.tik, p38.tik, mp40.tik) and open it with wordpad, but the hard part is putting it back in the right folder inside the pk3. the easiest thing to do is go to c:\ make a folder called models then one inside it call weapons, the extract the weapons you want to edit out of the pk3, edit it then go back to c:\ and put the 2 folders and file back in and presto you modified a weapon.