Why does my performance stink, despite having a more-than-capable computer?

My specs:
2008 Mac Pro, OS 10.8.5
2 x 2.8GHz Quad Core Intel Xeon Processors
12GB 800 MHz DDR2 RAM
NVIDIA Quadro FX 5600 w/1500 MB VRAM
1TB Hard Drive, 700GB open
Despite this, Final Cut Pro X is runnig like real jag. 3-4 times per minute it freezes for 3-10 seconds in order to sort something out, and it's even worse if I'm trying to preview titles or import audio files. I have turned off background rendering, I'm not using proxy clips, it's set to "Performance" rather than "Quality", and if I look at Activity Monitor while I'm using it, the whole computer is using about 20% of the total processing power and half the RAM. The temperature is holding steady at 90 degrees farenheit.
The project I'm editing has no effects, a few titles, and isn't even proper HD footage. I think it's 480i.
Any idea what gives? This seems a little ridiculous.

It is impossible to tell for sure. Performance of FCP X depends on a lot of factors, like CPU, GPU, RAM, Hard Drive, other programs that may be running, etc. 12GB of RAM should be plenty enough, unless you are running a lot of other things at the same time. Keep Activity Monitor open and see how much free RAM you have. If the slowness coincides with low free RAM, then quitting other programs and quitting and relaunching FCP X will help. But if there is plenty of free RAM, it is likely the cause lies elsewhere; then the drive becomes the likeliest suspect.
The system drive is used by the OS all the time, and that is the reason one should expect better performance from a separate drive (provided that the drive connection is fast: usually a second or third internal, if possible; for most users (i.e. those who do not have a Mac Pro) that would mean Thunderbolt, USB3 or FW800 in decreasing order of preference). But of course there is no guarantee because there may be something else on your system, possibly software, inducing these slowdowns.

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