Thanks for that Lefty. Just a couple too many pieces to keep track of it seems. I guess I need to make a list of all the bits that need to be in sync.
I think there are only three key pieces that the IDE uses from the board.txt definitions to use when compiling and uploading:
Processor chip type (needed to compile sketches correctly for the target chip being used)
Clock speed of the target (so some arduino functions like timer setups work correctly)
Baudrate to use when uploading (so correct speed is passed on to AVRDUDE commands)