Btw, Smoothie is not very good as a lot of people are finally finding out (here is just one example but Google to find more http://forum.seemecnc.com/viewtopic.php?t=10151 ). It is really quirky and does have issues with Thermocouplers. Now, a DUE based board will serve such a project better since the board will work "Dan Newman's fork of RepRapFirmware already supports up to four MAX31855 thermocouple interface boards connected to the SPI pins of the expansion connector." It is an ARM based board so will be a better solution AND is fully opensource so you can mod to your heart's content.

You might have ugly wires coming out of the printer but I can guarantee you the machine will run circles around what it can do now if anyone wants to ditch that Mightyboard setup and switch over to gcode and PWM that works for everything.