To upgrade your weapons you will need Antonio's Adaptation factory, which you buy from him, (Vendor Antonio Stacklund), it costs 512 creds. Once you get it, you will need to find an item depending on your type of weapon. If you ask him he will tell you what you need. But here is a review. When you find the items you need, you have to apply the adaptation factory on them, and then combine them with the weapon.

For pistols you will need a power supply, that you will get from the cargo droids, they are found on the docks. For SMG's you will need bone plates from the Malles found at the beach.  For shotguns you need a stalker's limb, they are also found at the beach.  For the assault rifle, you need to get a fluid sample, they drop from the waste collectors, that are found at the docks.  For the rifle you will need an optical enhancer, these also drop from the cargo droids. For energy weapons, you need to get the fuel chamber from waste collectors.

For swords, find the spine of a leet. For the broadsword you need to find salamander skin. For the bat, find the beak of a reet. For the hammer, the skull of a Malle. And for the dirk, some venom from the shore snakes.

For the grenade launcher, you need to get the compression chamber from waste collectors. For the shields, you need to find some salamander bile, from reef salamanders. And for the bow, you need rollerrat intestines.