For GC games to work the format of the HDD should not just be a basic Fat32 format but Fat32 with 32KB clusters, Windows can not do this without 3rd party software though
I can get into more detail for the other things later, I'm just doing a quick post between shifts though, so if you need any more info please ask away
I'm sure I can take you through the whole process of everything and have everything running from HDD without even needing a SD card at all if that is something you want