I think there could be 2 ways to repair:
1) based on repair skill
2) based on repair skill and exchange parts (so lets say when you click repair and youll be below a repair lvl to repair it, it will say in description "you need 1 MP (junk w/e)" then simply MP or any other thing should be placed in hand or be left in inventory and use repair skill, why not.
Now you can better make a new weapon than repair it while you have low repair skill (10mm pistol, lvl 1 weaps)