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Oh good to hear it works.
What pin are you using on the Mayfly.? I could see the references in the code on modemConnect() but couldn’t find any designation.
One of the problems is that the ATmega1284 doesn’t have any 5V compatible pins, so it may cause some unpredictable behaviour if it pulls the mega1284 pin up too hard – which depends on the Xbee.
One way would be to decouple with a NMOSFET with low drive voltage – eg with legs/TO92-3 TN0702N3-G – it turns on between 0.5-1V
It doesn’t need an R on the Gate where it interfaces to the micro, and probably doesn’t needs a pullup on the Drain, as there may be enough pull up in the Xbee – otherwise I would recommend a 10K-1M R. Its only activated for short period of time so the R doesn’t really matter – except it must be low enough to guarentee that the MOSFET turns OFF.