@Tim Edwards a question about GPIO[2-4]. I am currently using these as Inputs and assuming I will not need to program these on power up to be used as such as they are also inputs for the SPI. Is this assumption correct?

Yes, that is correct. You will, however, need to use the script

hkstop.py

that we have in the

caravel_board

repository which must be actively running to prevent the FTDI from driving those lines on the prototype board.