KERNEL

git clone --depth 1 https://github.com/raspberrypi/linux

Since I'm not including any custom deb packages, this is how I get the source. Only real difference is the Pi Foundation includes their own default config that's not in Linus' stock kernel, so before make menuconfig do a:

make bcmrpi3_defconfig

Everything else is normal (make, modules_install) until the last step which is to rename the /linux/arch/arm64/boot/Image file kernel8.img and put it on the firmware partition (mounted as /boot.)

OVERLAYS

git clone --depth 1 https://github.com/raspberrypi/firmware

It would appear the overlays are specific to a particular kernel version. So even with the latest firmware you should copy /linux/arch/arm64/boot/dts/overlays/ over to your /boot dir. I have to start all over with Mesa and VC4 because I neglected to do this.