I've been putting off putting a fan on my HR-03 Plus GPU cooler because it wouldn't fit unless I moved things around in my case a bit. That being said, I want to overclock to improve Crysis performance, and having a fan would be a good first step. However it's quite big with the HR-03 Plus + a 92mm Scythe fan. 7 cm to be exact (or ~2.76 inches). Currently on my GIgabyte 965P-DS3 I have 2 out of 3 PCI slots used. One for my X-Fi, and one for my USB card since I have a lot of USB stuff to plug in, in the 1st and 2nd PCI slots respectively. To make room for the GPU cooler I'd need to use the 2nd and 3rd PCI slots instead. Now my question is, if I were to move these, would they cause any problems? Should I move the X-Fi to slot 2 and USB to slot 3, or should I move the X-Fi to slot 3 and leave the USB alone? I don't want to cause any problems but I really would like to know ahead of time considering all the work I have to do to move everything. =\
Moving cards may require reinstalling the drivers for them. You should probably uninstall the device before moving it, as windows likes to leave old drivers in place otherwise.
If you really need more space you could loose the USB card completely and get hold of a USB hub or more USB backplane sockets (ebay is a lot cheaper than brick and mortar, and most online stores for things like these), and use all the headers on the motherboard. The DS3 has 10 USB sockets including the ones from pin headers.
Most devices use so little of the available USB bandwidth that an extra card shouldn't be necessary (unless you're using external drives in RAID or something). They're really only intended for older computers without USB or with just USB 1.1.
An electrical engineering friend recommended always putting the sound card as far from the CPU and Graphics card as possible, to reduce the electrical noise it picks up.
There's 4 on the rear panel and yes you're right, 3 internal pin headers. One of which I'm using for the 2 front panel USB ports on my case. However, where would the other 2 output to? I never even considered that idea before actually.