I have an Arduino MEGA 2560 and recently I have had a problem. I was using a super cheap SD card with an SD card module, and the SD card was so cheap it literally burnt part of it (I opened it up and inside it was a micro SD card). But, the SD card module stopped working. Now, when I bought a new SD card module, it still didn't work. I did some testing and I can't use pin 50 for digital writing or reading. I don't know if there is a way to change the pins for the SD card library on a mega, but however you can I need to do it.
My recommendation is to do some searching usng the terms:
"arduino" "software spi" "sdfat"
Since you can no longer do hardware SPI, you'll need to use software SPI instead, which allows you to use any pins on the Mega by "bit banging" the SPI protocol. SDFat is the name of the Arduino library that, from a quick search, seems to have this software serial capability.