Ah okay. Because I found that the default start order of gpsmon and chrony was incorrect meaning that the shared memory communications wasn't working but there were no error messages stating this. So sometimes, it would sync (slowly) and then chrony sources would say that it was having microsecond sync time but when I connected a switch (On/Off type) to the same gpio on two separate Pi's with linked earth connections and had a python program output the system time in nano seconds I found that despite telling you it was keeping time accurate to microseconds it was in fact many milliseconds out. The only thing I can conclude is that despite the setup indicating that it should use the PPS source that use the interrupt, this was in fact not happening and it was somehow getting it's time from the serial line only. Without indicating that this was happening.

When I switched the startup of gpsmon and the chrony daemon to the other way around time sync was achieved within 1/2 minute to a minute (Real fast) and the reported time on two separate Pi's with the joined up gpio's (So you can get very close to triggering a time check at the same time) was then sometimes as low as 30 ns's from each other, which is damn good considering that most of the difference would be jitter.

And none of the how-to's that I read talked about changing the start order of chronyd and gpsmon so I can only assume they all might be suffering from the same problem. It's important to note that the diagnostic commands from chrony will not indicate this and the only way you will notice if this is happening if you setup a rig like I mentioned above. I noticed because my sound localization calculations were showing errors that didn't make sense.