That might be it, I've never used a GCT with "Unknown codes" in it though so I wouldn't know. I don't think you can combine them, but in ASF1nk's thread all of his codes are there, so copy and paste those into a text file. Then, go get the codes from Mewtwo2000's stage pack and paste them in as well. Save it and open with codemanager, then export to GCT.
I heard about this a while ago, I'm glad at least a basic guide came out. ^_^ That being said, I doubt I could use it without a noob guide, like you siad.
Regular stages freezing too? That's odd. You sure it wasn't a hacked stage that was corrupted or something? If it's not the character, and the stage usually works fine, the only thing I can suggest is to reformat your SD card...
Are you using Riivolution? That's the only thing I can think of that might cause it..... If you aren't, try remaking your GTC, I guess. If charizard works on other stages he'll work fine on the custom ones.
??? Pretty sure thrownN bone doesn't affect throwing, aside from where your target goes. If everything needed a throwN there'd be no successful model imports. :/ Think of the Lloyd PSA, it has a shield, and I don't think the DotNW models have throwN bones. And you made sure you renamed the HipN, right? Sometimes Brawlbox doesn't save that kind of stuff properly.