the 96xx branch is EOL, it won’t be updated anymore. I suggest using the 3.4-lts kernel. Or you figure out how to compile the driver for newer kernels and provide a patch.
The driver is fine, as far as I know, its just the way its been packaged that’s not right. Certainly the missing link to version.h and the script error in conftest.sh are not faults in the driver.
The kernel changed. The driver needs to be adapted for those changes. The still supported branches (173.xx, 304.xx, mainline) will be updated by Nvidia in due time, but the 96.xx branch is EOL, so you’re on your own. You can try looking at the patches the community came up with for 304.xx and see if you can adapt them for 96.xx