If you actually play this game then you should know how the upgrades work. You find upgrade mods and pay for the upgrades. But to get easier upgrades all you need to do is go to a level that you beat and play it's minigames. They usually involve some kind of practice with either the wepon you gained that level or hacking.
Also you get upgrade points equal to the minigame level you are playing on for every rank E-B, but if you get to rank A you will get an upgrade for one of your weapons. An example would be if you played a level 3 game and got a C ranking for it you would get a total of 9 upgrade points. Three for each E,D,C.
But not all of the weapon upgrades can be gained this way, you may need to back track through levels to get more upgrade levels.
Also the best way to get rid of those pesky little bugs is to use the data launcer/sucker, not only do they die but you can use the stolen data to replentish your own heath!
Most upgrades for weapons are simple enough, all you have to do is;
1. Get used to hacking the little boxes hidden in each level 2. Get A rankings in the mini-games that you get after you beat a certian level (they are usually eiter time, health, hacking, wave, or speed trials. They shouldnt take more than 4 minutes to complete) 3. Or finding the gun's pickup (looks exactally like what you picked up to get the gun.)
Now here comes the hard part, getting the upgrade points to upgrade your weapons. They are usually found; 1. In hard to get to spots in the level 2. By hacking the boxes 3. Or by compleating the mini-games after the level (you get points according to your grade an what level it is. Like if you completed a level 3 mini-game with an B ranking it would show, rank E 3 upgrade points, rank D 3 upgrade points, rank C 3 upgrade points, rank B 3 upgrade points.)
By the way there might not be enough upgrade points to upgrade all of your guns SO USE THEM SPARINGLY!
Just one other tip To get all of the levels for your battle suit, beat the game