METROID DOOM MODDING DOCS
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This file will give you a basic rundown on some parts of modding Metroid Doom version 2 or higher.
This file is also very much UNDER CONSTRUCTION. ACS stuff is here, though, so that'll be helpful...

ACS SCRIPTING
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The following instructions assume you have basic knowledge with ACS. Learn about it on the ZDoom wiki.
ACS is handled in two different files per level: a global autoload.acs file and a per-map SCRIPTS (uncompiled)/BEHAVIOR (compiled) file.
If you want to change SCRIPTS/BEHAVIOR scripts, you need to copy autoload.acs to your ACC directory (contains zcommon.acs) using SLADE, 7zip, or any program that can open PK3s, really. Why? ACC expects #include'd scripts to be in the program directory, and GZDoom expects the compiled version to be in the mod. I know, it's weird. Whenever you modify autoload.acs, remember to copy the new version!

Simple instruction list version:
1. Make desired changes to autoload.acs
2. Compile into mod
3. Export uncompiled version to ACC directory
4. Make desired changes to SCRIPTS lumps
5. Compile SCRIPTS
6. Delete autoload.acs in ACC directory (optional)

Useful script numbers:
Give missiles: 4 or 19 (Best used with Missile Launcher/Tank thing)
Missile recharge: 7 (Best used with use-based linedef, or create a recharge station thing yourself)
Give Varia Suit: 11 (Best used with Varia Suit thing)
Give Energy Tank: 20 (Best used with Energy Tank thing)
Heat damage sector: 21 (Only usable with sectors)
Super-heated sector: 29 (Only usable with sectors)
Give Space Jump: 31 (Best used with Space Jump thing)
Energy Recharge: 33 (Best used with actor enters sector thing, alternatively usable with use-based linedef)
Enter water: 41 (Best used with walk-over linedef or actor enters sector thing)
Exit water: 42 (Best used with walk-over linedef or actor enters sector thing)
Gravity Suit: 43 (Best used with Gravity Suit thing)
Map station: 51 (Best used with map station thing, probably also usable with use-based linedefs)
There is a new cheat code that will automatically execute 11, 31, 43, and 51, as well as giving everything else, IDKFA-style.

Another useful script number is 666. This is the new external music changer script. It can be called as seen below:
ACS_Execute(666,0,newMusicNumber,musicName)
Where newMusicNumber is a unique number in the SCRIPTS lump (not the whole game) (this will only be run if newMusicNumber =/= the current musicNumber!) and musicName is the file name of the track (ex. Tallon Overworld 2 is D_STLKS3).

I highly recommend you use UDMF for future maps instead of Hexen format. Why did Spram do that for MAP01? No clue.
As of ver. 2.2, MAP01 is now available in UDMF format, too, under the name MAP01UDMF. This will become the main MAP01 in version 3!
I'll continue to add more script numbers as my future maps add new items/sector types/whatever.