This belongs in the general ROM hacking discussion thread, as opposed to here.
They are correctly registered, you just can't see them because they're not part of the Hoenn Dex. The easiest thing to do is to extend Ruby's Hoenn dex to include all the other Pokémon. I don't know precisely how to do that off the top of my head.
I highly doubt anyone will be able to help you.
And, so this post is actually on subject, these 2 hacks will probably have been of great use to many people. I hope you have more cool stuff up your sleeve, Darthatron!