If your shield says pin 10 is SD's CS, then pin 10 it is, so stop arguing. On Mega, I believe it's still the case that you set pin 53 as output , irrespective of whether it is being used or not.
So yea this all makes a lot more sense now. SS/CS is just for the Slave/Peripheral to know the message is for it. The "hey you over there!". Once this crystallised it all became pretty easy. (And the SS pin53 on the arduino is for when it is in slave/peripheral mode and not relevant if it is the controller)
I ended up getting a couple custom boards made and just physically routed pins to suit my needs in the PCB so I didnt have to use softSPI. Oh yea and the correct pins routed for 8bit parallel. The shield could just go bang on. Also added a level shifter so the SD card worked.

