Boot time on Mountain Lion
Since you have moved the system disk around, the Mac doesn't know where it is so it takes a few seconds to look for it.  You need to tell the system which disk will be the boot disk and where it is located.  After you have moved the disk to the bay, Open the System Preferences>Startup Disk window and choose the bay disk.  When you restart, the Mac will know exactly where the boot disk is and your bootup time will be a lot faster.