Now that I have seen the photo's of your case, it's become much more clear. This is what I would do :

1) I would mod the space where those two 80mm fans are in the front to make room for one 120mm fan. Those fans push a lot more air, so I wouldn't at all be surprised if one 120mm fan ends up to be more effective than two 80mm ones. (depends on what 120mm you buy of course)

2) mod the back of the case so that it can also hold a bigger fan. I don't think that a 120mm will fit there, but 92mm is certainly do-able.

3) mod the top blowhole so that a 120mm fan will fit.

If you use just those 3 fans, even at 5v, I can guarantee you than you case temp wil drop significantly. AND things will be a lot more silent too. The only thing you'll probably still hear is your HD.

On the page you linked, I think I like that 3.5" Nexus

That one is my favorite too. Especially since, like you say, the 3,5" bays are unused anyway. A word of warning though : the 5,25" version of that fan controller is known to make a high pitch whine when the fans are turned to 5v (low speed). Poor electronics if you ask me. But this 3,5" is a totally new version, so this may be remedied by now, I don't know. Just thought you might want to know that.

So, in short, thanks for the advice. Think it's about time I call up my buddy and ask to borrow his dremel tool

You're most welcome! These are really fun projects to do, especially when you get the desired results in the end. If you need any more info, just ask.