Some of the old RK weapons (most of which can be built from Manuals, found as loot on random mobs or simply rolled as mission reward) can now be upgraded. Each of them has several upgrades, so you can modify them to suit your skills. However, even if list include 120 weapons (you can find it by searching db for weapons which were modified in 17.6. patch), upgrades and skills needed are exactly the same for each type or main skill of weapon (for example Rifle) . And top quality of upgraded weapons is actually 200 (basic weapon sets final ql).
There are several ways how to get upgrades. You can buy it from Andre Bottle (only basic upgrades), quest for them from Engineer Heath Bridges or find them as loot on RK (confirmed drops from outdoor humanoid form robots and Bioarranged Beast - Model 666 mission mobs, there are probably more different types droping them). Upgrades need to be at least 90% ql of weapon and you'll need x5 in Weaponsmithing (last upgrade makes weapon Nondrop and takes no skill at all to apply).
The following table provides examples of different types of upgrade (scroll down to see how it's actually applied). The total number of weapons that can be upgraded is quite extensive. For a full listing if all upgradable weapons, you should search for "000" on AOItems item database site.
Process takes 5x QL of weapon in Weapon Smithing
Upgrades must be at least 90% of the QL range of the weapon you are upgrading.
And that's it really. Just remember that last Adjustment Kit will make the weapon nondrop. So if you're employing someone else to do other upgrades, just play safe and don't hand him last upgrade as well.