Chimera is using other bootfiles Gpt and MBR boot. I do not know how far the beasted install copy this files in these positions. In any case chameleon does not exchange this files, if they were found. I think they can cause also problems and should therefore be manually installed over with the correct chamelon files. Some time ago I tried the beasted method by myself on a sandybridge laptop and got nothing then HD3000 gfx glitches on my lappy. By switching to Chameleon, I got a complete messup of my install and I had to do a new one by making an usbinstaller in the conventionell way with Chameleon and some kexts. This went very well without any glitches in HD3000 gfx.
Since these days I keep my fingers away from the tools with the beast brand. This tools are having enclosed encrypted files (Look here: http://www.insanelym...14#entry1937842 ). Nobody knows, what these files are doing, execpt perhaps the developers. If you are using a device, that is created by these tools, you spread this information all over the inet. Look for example in an smbiosplist, created by that platform.
I suggest, that you should use your current install to make a new installer by Pandora. You seem to be skilled ennough for chosing the right options and Asus mainboards are well supported with this tool.
If your problems with the Appstore are not gone, you can get easyly the correct tips to solve your issuess with it.
PS: As fare as I can remember PCIRoot UUID and npci on chim... have other default values as Chameleon. They are set in this way for their suggested hardware. Perhaps your issue with your Apps downloads.