BlackShark

That file is empty (filled with FF).

27 Strange Ball 28 Poké Ball 29 Great Ball 30 Ultra Ball 31 Feather Ball 32 Wing Ball 33 Jet Ball 34 Heavy Ball 35 Leaden Ball 36 Gigaton Ball 37 Origin Ball https://github.com/kwsch/PKHeX/blob/master/PKHeX.Core/Game/Enums/Ball.cs

Save states are not save files and are not supported, save in game and open your save file. Besides that your PKHeX is very outdated, it even tells you there's a newer version available. You can follow the link in the program or get it from here:

Block 0 is intact at 0xA000 but unfortunately the recovery tool seems to clear it. Block 14 is the real issue it's missing/filled by FF. Here's the fixed save: ruby fixed.sav

Yes.

Well, the download for the patch from that site is expired. Maybe it's possible to just point the exit of Petalburg Woods to direct to the demo route instead. I don't know how complete it is or if there's more to restore. From what I have seen at least the trainers are there but Sharpedo and Kecleon are in your own party and I haven't seen any code for them. Ok, from what I have seen in the decompilation only the events (trainers, warps, signs) are still there. Anything else was deleted, even the map layout which was a bit different to the final one. You could use the final layout and move the events up by 6 to "restore" the route. There is no code related to Sharpedo or Kecleon left. I doubt that the Japanese RS has more code left.

Depends on what exactly you are trying to use. You can check how other projects are using PKHeX, for example: https://github.com/santacrab2/PKHeX-Plugins https://github.com/Manu098vm/Tera-Finder https://github.com/foohyfooh/PKHeXPluginPile https://github.com/arleypadua/PKHeX.Everywhere https://github.com/Bl4ckSh4rk/PKHeXWC3Plugin

If the ROM hack changed the save structure even PKHaX won't help. The best you could do is asking the hack author to provide a way to edit their saves.

PKHeX.Core.dll is on NuGet, so in Visual Studio you can just go to Project > Manage NuGet Packages. A window will open where you can search for PKHeX and install it.

Why are you compiling PKHeX? There is really no reason to do that. One of the latest commits a few days ago broke the compatibility with WC3 plugin v2.3.0. I am working on it but I will not release an update before the next PKHeX release. So if you want to use the plugin please wait for the next release or go back to the latest stable PKHeX 25.06.09 which is still compatible with v2.3.0.

You need to search for a specific species, you can't leave that box blank.

HOME trackers can not be generated, only HOME can do that, So yes, you have to put them into HOME.

PKHeX is a save editor, it does not "connect" to the games. You get your save from the emulator and open it in PKHeX. Read this:

Check the tutorials. There are different ways depending on if you want to use this on your 3DS or emulator: https://projectpokemon.org/home/tutorials/save-editing/managing-3ds-saves/