Does AGB-010 have the link cable passthrough? If it doesn't, I don't know how you'd connect the GBA with the card reader to a second GBA which would have the Pokemon game you are interacting with. I did re-confirm that GBA_Backup_Tool.nds works to restore the save onto an AGB-014 card reader...
Are you using the save file from the first post? How did you know you had an open party slot in the gamecube save if you had no colosseum to test it on?
1. Did your japanese colosseum save file have all 48 shadow pokemon captured/purified?
2. Was there an open spot in your party? You could also use the Google translator app on iPhone or android to translate what it is saying, which will probably help figure out what is going on.
Can you be more specific as to what you mean by patching your dev cart? Do you mean an actual development cart that Nintendo had distributed or do you mean something else (link ezflash etc)?
@Deoxyz given your impeccable track record, any reasonable person would trust your judgement and the judgement of the folks you are working with. Thanks for your willingness to come out of retirement for this.