Haus,
You are following the directions perfectly! The ExtRom does not mean it is an extended rom, that is just the nomenclature of the tool. the conversion from .nba to .nbf is a quick one. Copy that file to the flash utils directory and you can flash your rom!
The only way it would touch your extended rom was if you had an ms_.nbf in the flash utils directory as well (this is useful information if you decide to cook up an extended rom as well

)
Runt,
Thanks for the offer, but if i'm understanding correctly we will be able to use a ppcgeeks ftp shortly and in the meantime i think the torrent and rapidshare should be enough. Especially if a few that use the torrent help to seed it.