Should I rely on the EnergyShield2 for the RTC?
How do I power the microSD reader? Do I try and tap the power pin between the Arduino and the EnergyShield?
Throw that one out. There's no crystal so the RTC runs off the internal clock and is wildly inaccurate. I mean it loses or gains seconds per minute. It's enough to make it unusable.
I posted some code a while back that will correct it a little, but only if the board is running. It does nothing for it when the board is powered off.
If you have options other than the RTC on the R4, then use the other options. Forget the R4 has any RTC.