I verified that the configure script does not find libcap. Tried to apt-get install libcap-dev and configure again but it still doesn't find it. There appear to be a few debian packages out there for libcap but not sure which one it needs. I'm not super worried if chronyd has to run as root for my particular application.
I'm not exactly sure how to determine how gps-gpio is loaded. All I know is that I configured /boot/uEnv.txt to load overlays for the PPS pin and UART4. Then it was just doing apt-get install to get the packages I need. I ran dmesg | grep pps and got the following:
[ 1.538080] pps_core: LinuxPPS API ver. 1 registered
[ 1.538089] pps_core: Software ver. 5.3.6 - Copyright 2005-2007 Rodolfo Giometti <
giometti@xxxxxxxx>
[ 17.288476] pps_ldisc: PPS line discipline registered
[ 17.308702] pps pps0: new PPS source serial4
[ 17.308799] pps pps0: source "/dev/ttyS4" added
[ 26.049624] pps pps1: new PPS source ocp:bs_pinmode_P9_12_0x27_pinm
[ 26.049749] pps pps1: Registered IRQ 88 as PPS source
I'm going to try the slow deliberate approach to loading the packages to isolate where the problems begin.