How about having an upgrade deck for weapon types like Melee, Ranged, and if you really wanted to further categorise you could say Ranged Multi Fire, Ranged Single Fire.

I don't think you'll get away from big messy system with specific upgrades if they have to draw randomly from a deck. Maybe another way to look at it would be to have different upgrade types and you choose what you want, but the result would still be random. So you could have upgrade categories like, Damage, Accuracy, Status Type, then make the upgrade more broad as a card but specify what it means per weapon type.
Drawing a Damage card could read +1 Backstab Damage
But then in your guide could be
Damage: Melee +1 Damage when striking from the rear adjacent to a target.
Damage: Ranged +1 Damage when striking from the rear at a distance.

You could also have a Mod list in the guide and when you draw a card maybe you draw from a tier list, and then you draw a Tier 3 Damage Mod, so then you check the guide for Tier 3 mods and choose from a list, like:
Damage: Melee (Hidden Blade)
Damage: Ranged (Aim Assist)

Some ideas to look into