Hey mmcneil did you ever manage to find a fix for the embedded superuser problem, I am facing exactly the same problem as you with a nexus 5 self build.
My Build Powered by ArchiDroid Optimizations V3
Model: AOSP on HammerHead
Version: 4.4.4_r2 - KTU84Q
Baseband: M8974A-
Kernel: 3.4.101-TheArkenstone+
Toolchain: UBER-SaberMod-4.10_android-graphite arm-eabi-4.10
Toolchain: UBER-SaberMod-4.8.4_android-graphite arm-linux-androideabi-4.8
My Git: kidkoalauk github

JustArchi's ArchiDroid Optimizations JustArchi's ArchiDroid Optimizations V3 Git