Force Gun upgrade: In the Cargo Bay on the Hangar/Cargo/Tram Control deck.

Head through either of the two now unlocked doors against the far wall to find the Master Override box with the upgrade inside. Do this, and backtrack down the corridor and into the previous room with the big B symbols on the wall. Once inside the Deluxe Crew Quarters, you'll come to a circuit breaker that lets you send power to the doors. The easiest way to get this one is during chapter ten when you have to head there to find the shuttle.

Flamethrower upgrade: Inside the Deluxe Crew Quarters in the Crew Deck.

Line Gun upgrade: From the Hydroponics Deck central hub, take the door towards the Mining Tram Station, and you'll find a Master Override crate immediately in front of you with the upgrade inside.

Open the door and the box inside to find the upgrade. Move these out of the way to find the Master Override door to Tool Storage.

Contact Beam upgrade: When you enter the Mining Deck from the tram station, you'll find some slidable kinesis boxes.This is the same room where you got the Ripper weapon for the first time. You can find it inside the Master Override crate next to the upgrade console. Ripper upgrade: In the Machine Shop on the Engineering Deck.Here are the Master Override containers and upgrades I found:

To get Master Override clearance you'll need to complete the new 'You are not Authorised' sidequest, which involves gathering Crew Rigs across the ship. While there are upgrades and schematics scattered across the ship, the one guaranteed place to find them is inside containers or rooms locked with Master Override. There are two ways to get upgrades for guns in Dead Space: you'll either find the upgrade while exploring the Ishimura, or you find an upgrade schematic and have to bring it back to the store for purchase. There are weapon upgrades in most Master Override crates (Image credit: Motive)

Dead space 2 force gun schematic