I installed Flyakite yesterday. In order to get it working I had to reboot 3 times (once for iTunes uninstall, once for UXTheme patch and once for Tiger System Preferences). I noticed that my comp now doesn't boot half the times I turn it on (it shows the motherboard's logo and does nothing). Is this normal? 
Please help!
No that's not normal, try uninstalling everything and reinstalling it. Might even help to run a registry clean after uninstall with ccleaner, before reinstalling it.
I've realized the worst thing you could do after installing FAK and it does something like this is uninstalling it, at least most of the time. There's not much you can do now except for reformatting.
Well I mean it doesn't mess up my files or anything, it just freezes on startup. At least for now I've been able to start just by turning it off and on again, at which point the machine sort of turns on off and back on again, then the tower makes a beep noise, then it boots up fine. 
Going by what KAWSquared says, it sounds like you'd be best off backing up your files and then reformatting.
Wait... it hangs while at the mobo's logo, or after it? because it may be a hardware issue. Check your CPU's temperature and your power source voltage levels.
Of course based on your description it would look like FAKyte messed up your system, but it's better to be 100% sure to know what the problem is before proceeding. 
Well yeah it hangs at the Mobo's logo. it comes up and says "ASUS A7V400-MX" then gives me opeions for the BIOS menu and boot options but none of them work. I end up just turning it off and back on a couple of times then it works.
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