Related to the RTC, for use on a Mega; I made the cuts provided for A4 and A5 and then added wires to the Mega SCL and SDA. Of the 3 SC shields, one had a battery socket not soldered.
Related to the SD; I use the SDFat library. There is an example, ThreeCards which supports software SPI and it works. No cuts/jumpers needed.
Overall, initially I had intermittent operation of the RTC and SD on all cards. After a few physical removal/install of the shields, they worked. I'm attributing it to contamination on the pins which happens after PCB cleaning and general storage oxidation.