I've been adding in a ton of weapons, and unless I'm imagining things, they don't seem to interact with perks. Lever-action guns and revolvers don't get bonus damage from Cowboy and things like that. Again, I might just be imagining things (in-game stats are hardly transparent), but I wanted to ask, how exactly do mod weapons and perks interact. Is it automatic or somehow inherent? Is it impossible to make perks apply to created weapons, like how Grunt doesn't apply to the Bozar or 25mm Grenade APW? Or is it possible, but difficult?

I'm not trying to complain in some underhanded way, here. I just don't know anything about writing mods and I'd really appreciate it if someone could clear this up for me. Thanks for your time.

You need to add your weapons to the list of weapons that are covered by that Perk. Not exactly sure where to do that, but find the Perks, and then find the lists of stuff the Perks work on (Cowboy is one of them that will have a list) and you are there.

You will also need to make sure the load order is correct so your new list is not overwritten by another list in another mod. Or, use Wrye Flash or FO3Edit to Merge the lists.

They're called Form Lists and can be found under the Miscellaneous heading in the GECK menu, the one on the left hand side.