Rebuilding a the full linux kernel when modifying KVM for the purposes of patching VM exit RDTSC timings is a tedious process. Thankfully, the linux kernel is modular and can be built in pieces and incrementally upgraded.
This can be accomplished relatively safely by following the rough steps outlined below:
Fully build the kernel once, and loading this built kernel.
Compile only KVM as a module.
Kill all running VMs.