It's normal for a 68060 to identify as a 68040 under 3.1 as there were no 68060s in use when the code was written. Updating the CPU command, and the CPU libraries should solve this, but it shouldn't stop software from running at 060 speed.
As for both floppies, have you tried formatting one of the disks in one drive and reading it in the other? Maybe they were both badly adjusted in the past (assuming they came from the same source)
