Go to boss rush, scan for value 3, type is double, then f10 to turn on cheat, scan for value 9999, turn off cheat, repeat.
And BOOM, you got the damage multiply value. The address doesn't change when you exit to main menu and choose to play the story mode. In the story mode you still can change the damage multiply value to one shot anything. (the damage multiply value in story mode is 0, so it will change to 0 when you enter the mode)
EDIT 1: Doesn't seem to work with the machine gun.
EDIT 2: The health value for machine gun is 1100, type is also Double. Now you can freeze it and win the first boss fight easily.
EDIT 3: All values seem to be stored in float. And all initial upgrade values are 0 and can be changed, in cluding the pistol damage. What I scanned above is actually the pistol's damage level, and I believe someone can make a cheat sheet for this game. (not me tho, I just know how to scan)