Looks like the library does software SPI, so the pin allocation should be OK.
You have the Xbee module connected to the Serial port (as in hardware Serial0). This will be shared with the serial monitor port via the Mega's USB. Was that intentional? Looks like hardware Serial1 port is unused.
You are supplying the Xbee and RTC from 3.3V but interfacing them with 5V logic levels from the Mega. Have you checked if the devices will tolerate the higher voltage on inputs?
Also,DS3234: VoutH with Vcc @ 3.3V = 0.85 x Vcc = 2.8V.'2560 running at Vcc of 5V needs 0.6 x Vcc = 3V.So that'd be another reason to run DS3234 at 5V, or use level converter.Similar for Xbee - it's expecting 3.3V signals on Rx/Tx, not 5V.
Also, I can see a 22pF capacitor from 3.3V to GND near the RTC. I would expect a bigger capacitor(s) for decoupling.
Hi, have you tried all this out on a proto board first, stage by stage?It sounds like you are designing a circuit, getting a pcbs etched, then debugging.I would suggest you get a protoboard, get each feature of your project working, then on the protoboard combine them, each time debugging any problems that arise.With everything on the board and I understand untested it makes it difficult for anyone to help, as you have not told us if they work separately.Tom...... PS have you had previous experience with Xbee or RTC.