You might know this already, but, After Effects isn't designed to play back video in realtime. You're having a difficult time RAM previewing the content on your timeline due to the frame size, the span of time for which you are trying to preview, and the amount of available RAM to store the data.
Animation is a great lossless codec (at best/full quality), but the CPU cycles needed to decompress the lossless info does tend to slow down playback (i.e. - read time). You could try "None" (completely uncompressed), or perhaps Quicktime PNG compression (not an image sequence, but the PNG codec on a movie file).
You can also adjust your memory settings in the preferences to afford for longer RAM previews.
As mentioned, Animation is a lossless, very high quality and very high data rate intermediate codec.
Do you need alpha channel support? That will greatly change your codec options.
For no alpha, you could try the DNxHD codec http://avid.custkb.com/avid/app/selfservice/search.jsp?DocId=263545. Or use single pass VBR MPEG-4 at a high data rate.
If you need an alpha channel, the only game in town with real time playback on simple hardware is ProRes 4444 (only available with FCP).
It's likely that the reason it won't play back is hard drive speed. HD video, especially in uncompressed form have such a high data rate that unless you have a RAID setup you will never be able to play it back in Quicktime. You must render it as some sort of compressed form at a smaller data rate to be able to play it back.
but their doesn't seem to be anyway to get such a high res clip to play back the full length realtime in it's uncompressed format on my system.
...nor should there be. What you want is pretty much mutually exclusive. As the others already said, the data rates of uncompressed HD exceed your computer's bandwidth. The processor is utterly unimportant in that case, it's more a problem of drive speed, SATA bandwidth in combination with the PCI and memory performance of your system. There might be a chance to improve matters on one end by using RAID drives (4x striped, not just dual), but the rest is not in the users control. Therefore mildly compressed formats such as ProRes or the Cineform CoDecs are pretty much the only way to ensure realtime playback without extra hardware and staying in a production-ready quality. for normal verification and approval, just render out a H.264 at acceptable data rates, but of course don't work based on those files.
If you are on a Mac and own Final Cut Pro 6, I recommend Prores 422 HQ (output a RGB and alpha pass seperately). If you have Final Cut 7, you also have ProRes 4444 that supports alpha channels.
ProRes is designed to withstand multiple generations and supports 10 and 12-bit color depths as well as full raster 1920x1080 HD. And it uses no temporal compression. Compared against Animation or None QT codecs, it's a unbeatable tradeoff of file size, image quality,editability, with real time playback. ProRes 4444 is designed by Apple to be a replacement for Animation as it supports alpha, full 4:4:4 color sample, and higher color depths. While not technically lossless compression, you'd be hard pressed to notice any artifacts.