Should I be pulling in the source from apt and applying the patch that way? I am forced to use nvidia's drivers, and I fear the vanilla kernel may not work.
Ubuntu's changes to the kernel usually just backport new kernel features/fixes to an older kernel version. Compiling a fresh mainline kernel will get you most or all of those fixes. The source code shim that loads Nvidia's blob can be automatically recompiled by dkms when you boot into the new kernel. Installing the nvidia-kernel-dkms (or similarly-named) package should make that happen.