Indeed, since you have to do the fights anyway, so the items you get on the loot are like "bonus items".
The resources will work this way: during map exploration there will be some "resource nodes" which produce a certain kind of resource (food, water, energy, etc). Initially I wanted that to be just a goal for the colony survival, but then I also thought to make use of the resources to do some limited crafting.
Once you capture a node the resources keep producing each game turn/day. So in theory the resources is unlimited, but you don't have unlimited turns (after a certain X days the plot will advance).
Anyway I think will do as you suggested so the weapons produced will have fixed stats, maybe some randomized secondary ones, or depending what you mix in it. For example:
50 metal scraps + 25 toxic waste = 1 acid weapon with 50 dmg
50 metal scraps + 25 gharl stones = 1 energy weapon with 50 dmg
and so on, this way the randomness is very reduced, maybe just magazine size and reload but are secondary values and in any case are variations of a base value. For example sniper rifles have usually smaller magazine size than a SMG, so even randomizing those values you will never get a sniiper rifle with 50 bullets or a SMG with 5 bullets
Then also allow players to upgrade the weapons without spending all the resources again. For example the item above could be upgraded with only 5 metal scraps + 2 toxic waste and so on. I think this will be the best system