A guns modification basically overrides the existing gun cogs. So, if you want to change the concrifle and crossbow, make sure you have a folder structure like this:
Then just gob up your mod folder "YourMod" and load the gob in Patch Commander.
If you want to change weapon projectiles, too, you have to include a modified static.jkl in a subfolder called "jkl". It's probably best to download some existing mod and see how it's done there. Also read the tutorial about weapon templates here in the tutorial section.
If you want your changed weapon projectiles to appear in multiplayer games, you have to split the projectile generation code from the general weapon cog and call it by triggers. There are tutorials on Hideki's Millenium site about this issue (it's called client and server cogs or something).
To change weapon models is not difficult (eaving aside the actual model creation process). Just include your new models in a subfolder called "3do" (all textures of models go in a subfolder in this "3do" folder called "mat") and list them in the symbol section of your weapon cogs.
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