"Ok I do have another question...is it possible to say replace some of the say...grunts or sentinels with flood in 04_gasgiant? that spawn? How would I see the characters? Where do I find that order of characters?"
04_gasgiant doesn't contain any flood characters in the game file, you would be able to achieve this in the map 04b_floodlab.
To make this change, select a squad you wish to be changed into a flood character. For this example I'll use 'disposal_commander' 0-148 (the Spec Ops Commander). His character index is currently 10, changing this to 7 will make this squad spawn a single Flood Infection, you can edit the amount spawned through the normal and legendary difficulty count (Flood Infection spawns in a swarm). You will also want to change the primary weapon index to -1 in the squads box as well as team to player.
Here is a list of the character and weapon index values in a text document for this level:
https://www.mediafire.com/#xa30vq54h3mou
--
"Also..what does the "Major Upgrade" mean? Does it mean that the NPC's get upgraded in rank if I select the "all" key?"
This dictates whether all or some of the characters within a squad will receive a permutation upgrade from their base or set permutation.
So for example in a squad of Minor Elites, if the value is set to 'many' some but not all Elites in the squad will be set to Major or above (this also depends on difficulty played).
You can set individual ranks in the starting locations tabs in the actor variant spot.
To find the name of actor variants simply go to .char and select the character you wish to find the variants for, ie Elite.
You'll see a variant tab and it'll have two minor_scl and minor_dog.
Here's a list of all elite variants (not all maps contain them however).
Minor: minor_scl and minor_dog
Major: major_scl and major_dog
Specops: spec_ops_scl and spec_ops_dog
Spec Ops Commander: soc
Ultra: ultra_scl and ultra_dog
Zealot: zealot_scl and zealot_dog
Honor Guard: honor_scl and honor_dog
Stealth: stealth_scl and stealth_dog
Stealth Major: stealth_major_scl and stealth_major_dog
--
"And is it possible to mod where marines can wield brute shots?"
It probably is, I'll have to look into it ~~