(In regards to Hexerin's post, since someone posted between us.)
The problem then is you're nerfing weapons around the mods, which is not good. Honestly I'd probably say the effects of most mods should be reduced, and base weapons should be brought into line disregarding mods.
If this somehow ended up being something I could control (which is likely a terrible idea), I would probably remove mod ranks entirely, and just have one version for each, with a power level, probably roughly around the level 2 mods. CJ would be 5%, IR would be 5m, etc, and then simply spend time increasing the available variety of mods, rather than trying to strike a balance between multiple levels of the same thing.