I’ve been looking over the schematics and the nano seems to be missing pins d4, d8, d2 ETC. So is there no way to hookup thses two boards or can I reassign these pins to have the same functions as say the pins on the redboard? I need the formfactor of the nano and have shrunk the canbus board to a db9 connector wide form factor dropping off the sd card and other functions as I just need the can ability. None the less documention leads me to believe this may not be possible and I will have to design my own board to use the pins that I need but hopefully one of you might have an asnwer. Thanks 
The artemis is a fairly advanced board and might not work with sparkfun’s libraries directly. It would be possible to use other pins, but you’d need to consult the data sheet for the apollo3 and to see which pins would be the best to use on the artemis nano.
It might be a lot easier for you to use something like a 5 volt Pro Mini, it’s small but 100% compatible with code written for the Uno the can bus shield was designed to be used with. And it has all the same IO pins that the shield is looking for as well.