I've installed the 10.6.3 OSX update without any issues. However there seems to be some change in the screen colours which will require a fresh profile of my MBP display.
It doesn't matter in which order you apply the updates, one is for the core OS and the other is for Pro Apps, well that's my understanding.
Since installing the ProKit I've found Aperture runs better, no slowdowns after heavy usage. Available memory seems to remain available.
I have my own suspicions about the problems with Aperture. I had a new Mac Pro onto which Aperture 2 was installed. I installed Aperture 3 Trial form the Apple website and everything worked fine, no stalls, no hangs. I deleted Aperture 2 with clean my mac and I deleted some files I shouldn't have rendering the OS buggy. So I wiped the System.
I did a fresh install of the OS with the provided DVD's and updated everything than installed Aperture 3 from the DVD I had bought. And the nightmares began, sharpening caused crashes with alarming regularity and brushes did the same. I wiped the system again and did another fresh install from the DVD's and had the same issues. Finally I wiped the system again installed the OS from the DVD's, updated everything and downloaded the trial Aperture again form the Apple website and everything works perfectly. Go figure that!.
Peter, I'm sure Apple would have liked more time to polish Aperture 3 before they released it. I'd suspect pressure was brought to bare by the user base who saw the Lightroom Beta release and were decrying the lack of information about the rumored Aperture 3.
Incomplete or complete, it worked for me first time round, but then again for the first time in my usage history of Aperture 1, 2 or 3 I had sufficient memory, processor & graphics horsepower to run the application smoothly and without issues. It seems very stable now with the 3.0.2 update and the ProKit 5.1 installed. It might just be the right time to move over to Aperture.