you can allways set it in programming mode by:
press and hold flash button
press and release reset button
release flash button
you can do this if you see in the status window that the flasher has problems
in general all gpios should be safe to use as long as you satisfy the necessary level at reset time for the gpios allready mentioned by martinayotte (0,2,15).
gpio9,10 are not to be used also as they are used by the flash chip (allthough there are hw mods to use them).