I followed the instructions to stop my array, open the flash, and copy over bzimage, bzroot, and syslinux.cfg from the new 5.0.4 over to my flash and overwrite what was there.  However when I reboot my version is still reported as 5.0rc12a.  I looked at the dates on the bzimage and bzroot and the timestamps seem to match what was already there according to my flash backup.    Any ideas?

Run a disk check on the flash drive. It sounds like you may not have ejected the drive properly, possibly pulling it out before the files actually completed writing.

It was done over the network share mounted to /flash, I never removed it from its home.

There may have been a mistake or a hardware fault. Try again.

Actually it appears my Downloads folder that I was using to extract the zips from was corrupted.  Even though the filename was the 5.0.4 one it was still opening the 5.0rc12 file.  An MD5 on the zip revealed them to be coming out to be the same in my directory.  The strange part was the 5.0.4 filename was reporting a date modified of 12/7 like it should have.  After trying to delete the files, my computer experienced it's first hard lock in the 2 years its been up.  I had to chkdsk the drive to even be able to access it again.  Upon downloading again, everything seems good to go.  Stranger things have happened, but this is up there for me.