PKSM VS LumaLocaleSwitcher

PKSM is a save manager for Gen 3-7 Pokemon games. (Gen 3 games can be installed to the 3DS's internal memory like Virtual Console games, but you can't use the normal multiplayer features.) You can use it to generate/modify/clone Pokemon, but you can also just use it like an offline version of Pokemon Bank. It lets you move Pokemon around freely between games, well beyond the scope of official tools. There's a wiki link somewhere on that Github page that'll do a better job of explaining the features than me.

Simplest, use PKSM to transfer Pokémon from your Gen 4 cart to a 3DS game, then transfer to Bank from that 3DS game (assuming you want to go to Switch games, if all you care about is getting them on the 3DS game you never even need to use Bank)

Click on this. how to download pksm

This is the way. A tip, you have to tell PKSM where the save file for the game is. You can do this in the PKSM options under "Extra Saves". https://github.com/FlagBrew/PKSM/wiki/Settings

fyi there's also PKSM which is basically PKHeX but on console.

I wouldn't recommend it, just to be safe. I would try with PKSM, an application developed by the same folks behind Checkpoint.

I assumed you're on DSi because you said "DS XL" and that isn't a thing so I figured DSi XL, if you're on a 3DS XL though you'll actually want to use PKSM, it's basically the same thing but a bit better as it runs in 3DS mode.

I would recommend homebrewing your o3DS, using GodMode9 to back up your DSiWare game and save, and then transferring those backups to your N3DS LL. Additionally, even after a region change, many games, apps, or settings will still be in Japanese, so I would recommend using LumaLocaleSwitcher to further change the language/region.

Download Luma Local Switcher here

Not 100% sure about saves... but I think it'd be OK. The utility is Luma Local Switcher.

You need to use Luma Locale Switcher: https://github.com/Possum/LumaLocaleSwitcher

The one caveat is that sometimes games that are "regionless", e.g. Rayman Origins, will ignore the console setting and use the original language of the console. You'll need to use Luma3DS locale switcher (https://github.com/Possum/LumaLocaleSwitcher/releases) combined with game patching enabled in the Luma CFW to force it onto English.

Some non-Japanese games will also continue to display in Japanese or will freeze/crash if you do not region swap the console, in which case you will need to use Luma's built-in Locale Emulation (covered a bit over halfway down the page here) or LumaLocaleSwitcher, possibly a combination of both.