Actually initrd related. The new initrd for the new kernel had none of the old cruft from the partition change and such. It was made with the system in its present form.
Ran this command as pags suggested:
mkinitrd -f /boot/initrd-220.127.116.11-pclos6.bfs.img 18.104.22.168-pclos6.bfs
As su in root terminal it completed the command with no errors or anything
but the 1 minute timeout remained. Only thing that doesn't make complete sense.
I change flash drives frequently but rarely do I change a 3rd partition to a first partition
to run the OS. So, in the future I know what to do if I'm looking at a slow boot from that.
Booted up this evening just perfect so I'm marking it solved.