Adjustment brush (retouch) slow to the point of being unsusable

Question

First, system and config info:
Mac Pro (2 x 2.66Ghz)
6 GB RAM
ATI Radeon 4870 w/512MB VRAM
OS X 10.6.2
Aperture 3.0.1
Aperture library is on a separate disk from the referenced images. Neither the library nor the images are on the boot drive.
My test image is a raw NEF file of a waterfall with some graffiti on nearby rocks. If I send the image to Photoshop CS3 as an external editor I can stamp/clone a layer to brush out the graffiti and the response is, for all practical purposes, instantaneous. If I use the "retouch" adjustment within Aperture 3 in "clone" mode, I get a the dreaded spinning beachball and a "loading" pop-up. The response is so slow that it is very difficult to make any sort of fine adjustment.
FWIW, I have been using Adobe Lightroom for the past couple of years but decided to take another shot at Aperture (I had tried v 1.1 but did not like it) because of the new features, especially Places and the new targeted adjustment tools. However, the adjustment tools are just dog slow even on a pretty well configured system. If I have to continue to do a round trip to PS CS3 for adjustments because of the dreadful performance in Aperture, then I may as well stick with Lightroom. (I can't imagine what Aperture would be like on my MacBook Pro....).
Anyone else having performance issues with the adjustments tools? Any ideas to improve matters?
Thanks

Answer 1

I have tried a number of the suggestions in other threads.
The Aperture libraries are on their own separate disk. They were created from scratch, no import of older libraries. The images were imported and left in place (referenced). After a couple of weeks of use, iDefrag shows almost no fragmentation in the libraries (0.02%).
I have done nothing to specifically start OS/X in 64bit mode. I don't see the point. The only thing that is likely to happen by forcing this is to break things. The OS is "as installed", as is Aperture 3.
The GPU is the fastest that I can get to work on my generation Mac Pro (ATI 4870).
Suggestions to clear cache and prefs, given that this is a clean install of Aperture and the libraries have been created new, from scratch, seem pointless but have been done anyway in the interest of completeness.
Energy saver has been tweaked to disable spinning down the disks. In fact, since I use Final Cut Express occasionally, I have implemented the config steps suggested by Tom Wolsky in his excellent book on that application.
At this point, I have no more spare cycles to spend troubleshooting Aperture. I am falling back to Lightroom/Photoshop. I'll circle back later, if/when Apple gets this version of Aperture sorted out. I really want to use Aperture. I like its interface and DAM model. The native targeted adjustments are a compelling feature as is Places. And the integration with the rest of Apple's application ecosystem is a big plus. However, it is hard to get past the dog-slow performance on pretty powerful hardware.