hellomynameisphil
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hellomynameisphil's post in boot-update doesnt see 4.0.1 was marked as the answer
Figured it out.
I generally have /boot on a separate partition. This partition seems to get unmounted automatically after booting is complete. So when I was compiling 4.0.1 and installing the linux kernel binary, it was to a directory called boot in my root file system which is inaccessible when the boot partition is mounted on /boot.
I am typing this from 4.0.1. Thanks to all who made suggestions.