Eelhead - which ones are the shorter standoffs? Currently I've got the ones with the little "bulb" on the top, and the other ones which have an opening for screws. I've tried the ones with screw openings but I seem to be about a millimeter or two too high for my PCI slots :(
They are too high because they were originally recessed into the material of the case (by about a mm). However, it doesn't matter that there is a mm of height difference. You can always put a thin washer under where the card fixes to the screw hole of the PCI slots if you are worried.
Water Cube: Zotac Z77-ITX WiFi - i7 3770K - Radeon HD 7750
Mac Pro Mod: GA-Z68XP-UD3P - i5 2500K - GeForce GTX 660
Ahh, forgot about the recession. I quickly filed down the tops of the standoffs with my Dremel tool using the sander attachment, they're fitting perfectly now. Thanks guys, I should be done with the entire thing today!