We've been doing a lot of work on this project behind the scenes on GitHub - upgrading the code with better parsing routines that no longer use strings. One of the aims is to reduce the complexity of the control system and as a result, increase it's reliability.
Very soon, the Nano MCU that receives the FONA data will be removed and data will be collected by the Mega instead. It may be that the machine needs to physically stop to avoid interrupting the GNSS data stream but probably not! Worst case scenario is that the machine stops and downloads the next 10 or 20 waypoints.
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