I have built an NTP clock using yocto fido. It includes the PPS interface and provides microsecond accurate timing to my home network.
You can grab the following:https://www.dropbox.com/s/1z4zr7kvhamsg ... ar.gz?dl=0
In that tar you will find meta-falco which includes my patches. You probably won't need all of them, as I also hacked ntp to display the satellites, signal strength, etc. on the touch-screen. I used a 3DR GPS module. It contains a uBlox chip, and while they don't advertise the PPS connection, I was able to white-wire it based on the uBlox datasheet.
I used TP126 for PPS input GPIO (2,13), which is pad SD4_DAT5.
I also added a chronodot to provide a battery backed real time chip. I wired that into the same I2C bus that the audio chip uses.
There are a few other files in the tar that you will need. bblayers.conf is what connects up meta-falco, and local.conf brings in pps tools that are handy for debug.
There are also a few jpgs that show what the display looks like and some of the white-wires.