#1. Just use the Maxxuss Patcher GUI instead of AMD Patcher, it's the easiest way and everything should be OK. To check if CPUIDs were patched successfully, simply launch iTunes and check if there are no blank windows (when I launched it without applying the cpuid patch, the preferences and "get info" windows were empty and iTunes crashed when I was trying to log on into the store).
#2. As for the dark graphics, go to "System Preferences" -> "Display" -> "Color" and check different color profiles, maybe the one you were using was just updated.
#3. As for now, you can install all the updated in Software Update, even those which require reboot. At least I have and it seems OK Just be careful if eg. 10.6.5 update comes out, because it may install new kernel so you may be unable to boot.

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Gone Linux.