How to get the ultimate upgrades:
Act 2:1: Flash Freeze (Flash) - Complete all 3 Hollow Storm Locations
2: Seeker (Shock Trap) - Complete all 3 Outsiders Locations (Loot the Safe in North Tower Sub Station)
3: Marked for Death (Pulse) - Complete Condor Crash Site (South - Loot the safe at the end)
4: Brawler (Stim) - Complete Condor Crash Site (North - Loot the safe at the end)
Act 3:5: Detonator Implant (Hijack) - Complete all 3 Scavenger Locations
6: Slayer (Cloak) - Complete all 3 Waterworks Locations (after you complete your last location, pick up the upgrade from Paduk's Nomad Guy)
Act 4:7: Deadly Overload (Barrier) - Pick up in chapter 4-1 in the Swarmak fight area
If you need a visual location for the last upgrade, look into the spoiler