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I was wondering, if a pokemon in GEN3 gets a portrait in the Lilycove Museum (after winning a master rank pokemon contest), does its data get stored as it does in the Hall of Fame? It does show that the pokemon is shiny, for example. So I thought that maybe it stored PID, OT and more as the Hall of Fame does. Sorry if this isn't the right place to ask this, I wasn't sure where to ask about it.

I suggest you to download the Auto Mod Plugin for PKHeX. In the plugin menu there is an option to generate a full legal Living Dex. You can personalize nature, ivs and evs with the batch editor of course.

Looks like they decided to do something against hacking. Don't know if it's a good news.

FYI I worked it out! Did some editting on the Regigigas script and manage to get my script working. Basically now if you have Tornadus and Thundurus in your party and visit the Abundant Shrine, the Reveal Glass event will now play once. I have also made it so Landorus appears after a white flash, once the man moves off screen after giving you the item. I am happy to share the Script and Overworld file for it if needed. I will in the future change it so Landorus flies down to the shrine like in BW1, I will look into how I add that movement in after my previous attempt failed.