Well here's the thing, it does work when wired like this. I simply clipped the header pins at location 10,11,12,13 and wired in 50,51,52, and 53 from the MEGA. Using modified code from the sparkfun can-shield the board works just fine like this. I can read and transmit CAN from the MEGA. The problem is i need 29bit CAN which the sparkfun code does not have provisions for, it only does 11bit.
That brings me to the original seed studio code which does support 29bit CAN. It works great on my UNO, but i need the extra serial ports on the MEGA for other stuff. I know this wiring works because it works with different code. I just can't see how to get the seed studio code to use the other pins for SPI. I tried following the code through SPI.H and i see where it references MISO, MOSI, SCK, and SS in the pins_arduino.h file. I see after i compile that it infact looks into the \variants\mega folder for this file. So everything should be right, i just don't understand why it's not working. Yet, the arduino UNO works fine?