How to generate linux-tools packages for customized kernel?

The build target you're looking for is binary-perarch:

$ fakeroot debian/rules binary-headers binary-generic binary-perarch skipmodule=true

Somewhat related links:

  • https://wiki.ubuntu.com/Kernel/BuildYourOwnKernel
  • https://wiki.ubuntu.com/KernelTeam/KernelMaintenance

Simply execute

fakeroot debian/rules binary

This will create all of the debs, including tools, cloud-tools, lowlatency kernel, etc. It doesn't take much longer, and prevents headaches.