This sort of thing just happens when Chameleon/Chimera wasn't installed properly, for some reason or another. Reinstalling the bootloader (like you did) usually fixes the problem.
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What fixes are you referring to, specifically?
Try using a different USB drive. USB drives vary in quality greatly; I once tried installing Unibeast on some shoddy USB drives I had picked up from China a few years earlier, and the Unibeast installer struggled for 50 minutes with them until it finally gave up. Then I tried it again with a...
Generally, Gigabyte motherboards are recommended because they work with sleep mode and CPU power management in Mac OS X by default. Motherboards from other brands need a patched BIOS; it's not particularly hard to flash your motherboard's BIOS, but some see it as an unnecessary extra step...
I don't think the WiFi from the motherboard is supposed to work. On Hackintoshes, it's pretty much extraneous.
The 41 GB problem is really weird. You can use something like Grand Perspective to see what parts of Mac OS X are taking up the most space, though.