Great start to the fic, I've always liked Overlord crossovers. As for the fifth hive I guess you could go for the obvious route. Make it so House Elves were once part of a Hive but maybe it got stolen or hidden long ago by wizards during a fight with a previous Overlord. Without a Hive to draw energy from they had to bond to wizards or die out.
As for their powers you can either keep them as they are (meaning magical house keepers) or make it so their current powers are the product of the energy they get from wizards whereas they have a different set of powers with the energy from their Hive. Which might make it an interesting choice for the elves in question, do they keep what they have and just bond to Harry (since he's a wizard) or do they re-bond themselves to their Hive and loose magic? Maybe have the elves split factions with some doing each.
With the Hive species being the elves it could also allow you to tie Hermione to Harry's cause in a round about way. I could see Hermione finding out about the elves origins in a book and deciding to try and find a way to get the hive back so the elves can "live free". Maybe have her go into a research binge and not telling anyone about what shes working on as it would be against the law if she actually did find a way to free the elves.
Could add a bit of mystery to things with Harry trying to find the Hive and trying to figure out why Hermione is being so secretive.
Anyway sorry for the ramble. Thats all I can think of right now anyway. Its late and I'm getting tired. Keep up the good work.
Thanks for the reply. Personally, I don't see the house-elves related to the Minions, despite their common appearance. Thanks for the idea, though, and I'll keep you updated as often as I can