First of all, hello and welcome! New modders are certainly encouraged to ask questions so feel free to lay them on us. I haven't even been here a full 10 months and already I'm very well versed in everything battle-related.
Let me try to answer some of your questions:
1. Hojo vs Proud Clod: I don't want Proud Clod to depreciate Hojo like what WallMarket did to Teioh. Squall has done good work with Hojo and I'm just picking up the pieces and filling in some of the blanks. Yes, the scene numbers are off. This is more Squall's choice, but the game refers to them as 0 - 255 so that's how PrC (the abbreviation for Proud Clod) is referencing them. PrC isn't very pretty yet. There's still a lot of labels to be made. BUT, it's the easiest way to edit AI and battle data. I'm not bragging, it's just fact at the moment. Keep up with it too. It's still a WIP. WM's almost done, though. Almost all that's left is fixing bugs and finding values for currently unknown things.
2. Edit AI: Yes, this is complicated. If you've played around with FF3USME (which is where I stole the idea from), it's nothing like that. It does require some basic programming/logical-level thinking. There is some good info in WallMarket's readme about how to write it as well as some examples including how to use most of the opcodes. Just keep in mind that the disassembling isn't always 100% accurate. Compilers know some tricks to turn script into oddly written code that makes it more efficient. When this happens, there's almost no way of returning it to its original code without knowing all these tricks. If you're stuck with how to do a particular thing just ask. Most of the modders (at least the ones that have made enemies) are able to help.
To get your weapon to start out with Level 3 Death there are several things you need to do.
#1. Create the attack data in the scene: Take a blank attack and give it the data that resembles Level 5 Death (use WM to compare), but make the Hit% a 3 instead of 5.
#2. Give the attack a unique ID number. PrC can give you a list of IDs that aren't being used anywhere in the scene.bin, but it would probably only need to be unique to that particular scene. Just make sure it's above 100h or the game will use the attack data from the KERNEL.BIN.
#3. Assign the animation. This is what the animations/formations button is for. Tell your monster that you want it to use animation index ## for this attack. Most enemies have at least four animations, many have more. Idle*, Death*, Damage*, Attack, Magics, Special Movements, etc. (*they'll need these at least).
#4. Write it into the AI. This is where it starts getting hard. You'll need to look up the usages of all the codes before you write it. Also, you might want to keep the ProudClod.dat file open so you can see the addresses that are used for particular functions. This script would go in the Pre-Battle:
12 2070
02 20A0
90
60 20
61 ####
92
That will cause the enemy to perform whatever attack has the index of #### on all if its enemies (all the player characters) when the battle begins.
Most of the features of PrC are in the topic about it. The animation assignment is particularly important. Don't give an attack to an enemy without giving it an animation.
3. Scenester works in conjunction with SceneReader. SceneReader can separate all the scenes in scene.bin and write them back together. This is a requirement for Scenester and SceneEdit, but PrC doesn't have such dependency. It works with the scene.bin directly and update the KERNEL.BIN.
4. Just as a suggestion. As most people suggest actually using KoR on Ruby/Emerald, it doesn't make a lot of sense to make it a requirement to fight something stronger before you get it. Maybe something to fight as you leave the cave AFTER you pick it up would be more appropriate.
As a first goal you set your sights high. Not to say it can't be done. It can. But it's likely going to take some effort.