I wanted to resurrect this particular thread because we have been running into the same issue that Chan had. However, I note that there is a new variant of the SDI12 library as of roughly 2 weeks ago (EnviroDIY_SDI12_PCINT3) and I am pretty sure that it is an updated version of the SDI12_mod that Shannon sent in response a few years back in this thread.
We are going to work on this because we are interested in having the Mayfly control several SDI-12 sensors in a remote field site using the RTC to put the logger to sleep in order to only collect measurements every hour.
I get the sense that that is what the water monitoring project around the Delaware River basin is doing, but it is tough to know without looking at the code. Our network will be in remote northern NH.