thats what you really need when you want to use the old files. And after that is translation.
Since its quite really old files, so maybe you can do some reading at zackdreaver translation https://github.com/zackdreaver .
Client also still listed at NEMO : https://nemo.herc.ws/downloads/#2012 but as u said you already have that EXE. You just need to patch/hex it then.
For Weapon Generator, I've add all the possibilities of Weapon Type that I found in existing weapontable.lub so you can choose either one that suitable with custom weapon that you're going to add.
1. there is a lot of tutorials, maybe can read if u are using Chris Translation, but the info are already well enough https://llchrisll.github.io/ROTPDocs/guides/basic_custom/
2. there isnt. you might need to know which npc was there, or not and disable it. Maybe some changes too outdated one too if going to old episode.
3. conf/battle/ you might see most configs there.
Depends on how do u want it. download new and start fresh.
OR
You can also update your rathena and also all related databases to match to latest rathena.
Note: The new skills of Dragon Knight (Dragonic Breath), Biolo (Explosive Powder, Mayhemic Thorns), Meister (Mighty Smash, Spark Blaster, Triple Laser) need a client 20220602+.
I think what you use is client 20220406, which is April 06, not June 02.
u are using palette from who, and did u read the required files to use that palette ? doesnt need those patch though.
If u didnt, read back what the required files from the palette.