1/ If it's an 80 pin ribbon then yes. You can tell if you compare it to say the one on your cd drive, the 80 pin ribbon will look 'finer'.
2/ The normal way is to have the hard drives on the primary channel and the removable on the secondary. Within these; the faster, and most used drives should be the master.
Therefore, your suggestion would be the best all rounder.
Finally, no, it shouldn't really affect performance if you use differnet connectors for slave and master, but if you have blue connector on your HDD cable, it MUST go onto the mobo.