Nothing that appears GPU related, looks like your USB devices might be ejecting on sleep, maybe just the UHCI (USB 1.1) devices, USBBusFix is supposed to fix that if DSDT doesn't. Most patched DSDT only have extensive edits for EHCI and sometimes UHCI gets overlooked, which has caused some problems in ML for people where in Lion it was not a problem. I use it because for some unknown reason it also increases my benchmark scores 5-10%. P&C states or Cstates using sysIO would apply to speed step, which can also be enabled via DSDT and/or SSDT. If you have HWmonitor installed with FakeSMC monitoring plug-ins, there is a CPU frequency option where you can see it go from the low x12 multiplier to whatever you set as your high multiplier in bios. Even though you'll likely have more than 2 states enabled, it will only show the high/low but in graph view can see it hitting the different states in-between. Try with and without P&C states and see if any difference in this behavior and if any difference in the cpu temps. Prob don't need force HPET, but won't hurt to use it. If you use the Perl command I posted a few posts back, that will patch AppleRTC. Some systems if using MacPro 5,1 smbios will KP during boot from AppleTyMCE, so you would know if you need to remove it
Here's my org.chameleon.Boot.plist, some of which is not 100% necessary and graphics stuff specific to my card, UUID stuff specific to RAID-0 booting:
<dict>
<key>AtiConfig</key>
<string>Uakari</string>
<key>AtiPorts</key>
<string>4</string>
<key>Default Partition</key>
<string>hd(0,3)</string>
<key>DropSSDT</key>
<string>Yes</string>
<key>EthernetBuiltIn</key>
<string>Yes</string>
<key>ForceHPET</key>
<string>Yes</string>
<key>Graphics Mode</key>
<string>1440x900x32</string>
<key>GraphicsEnabler</key>
<string>Yes</string>
<key>GUI</key>
<string>No</string>
<key>Kernel</key>
<string>mach_kernel</string>
<key>Kernel Flags</key>
<string>rd=uuid boot-uuid=92496DB5-5DB1-365B-B82B-533C19F4945B -v npci=0x3000</string>
<key>SystemType</key>
<string>1</string>
<key>Timeout</key>
<string>3</string>
<key>USBBusFix</key>
<string>Yes</string>
<key>UseKernelCache</key>
<string>Yes</string>
</dict>
Disabling the pretty GUI speeds up the Chameleon boot time between selecting boot drive in Chameleon and Chameleon's pass off to OSX bootloader quite a bit. Also purposely using wrong resolution for Graphics Mode because if I do enable the GUI, LogIn to Lion theme has a artifact in bottom right corner at 1920x1200.