What would be signs of the QE/CI not working properly?
When you move windows around does your CPU use spike? When opening new dashboard items on the screen do you get a smooth ripple effect? I've been running a 4890 for years and every time Apple pushes out an OS update I have to grab the corresponding QE/CI patcher. Unless you're running a really off reference 4870 you shouldn't need to do this.
I don't have to use a theme... I just thought it was an option
Using a theme is an option but if you're reporting problems with them why use them?
Before I checked darkwake, it would freeze after wake. I'll uncheck it and see what happens.
The hard freeze is a known issue and so far has no fix I've heard of. Personally I just disable system sleep in the Energy Saver prefs.
I didn't use any EFI patch to the cards ROM. If I'm not having graphics issues do I need to?
Then how, may I ask, did you flash it? Previously the only way to get the grey Apple logo on boot with a PC card was to flash it with a modified ROM that included the EFI code.
I must have neglected to copy the dsdt.aml file. I do have it though
That right there will solve a number of your problems.(How have you not had audio issues?)