What version of Mountain Lion are you using?
To fix the NFTS-fs warning you have to run a full CHKDSK from windows.
In safe mode you have to install patched kext, dsdt, multifail... to make it work whitout boot flags.
To make USB 3.0 work, you have to install usb legacy from multifail, and for touchpar install elan touchpad kexts.
If you are using 10.8.2, you will have a lot of problems, use 10.8.