Hi stinga,
I get the impression that you have a firm basic handle on stuff. Personnally I am a bit of a glutton for punishment and here would be my approch.. just to offer some food for thought.
Take your current system and do a good back up, follow tjc's suggestions to also do a backup of the "special stuff" you have done. Then you have two, one standard, one enhanced. Make a copy of your /etc/fstab, especially the line for the /dev/sda_ /myth write it down on a piece of paper. Oh energy conservative huh? Then add this line and then poke in a memory stick.
/dev/sda1 /stick vfat defaults,user,noauto,showexec,umask=022 0 0
mkdir /stick
mount /stick
cp /etc/fstab /stick
cp /<anything-else-you-want> /stick
umount /stick
remove stick
Then disconnect the drives and put in your new drive and install the R5A22. At this point your system is close to original without the tweaks. Since your backup is on the serial drive, you would nead to edit the /etc/fstab to gain access to the serial drive however edit the line to be mountable as /old-myth
mkdir /old-myth
While you are there add the line for the /stick and
mkdir /stick
plug in stick
mount /stick
now you have access to the old saved tweaks and files
mount /dev/sda_ /old-myth (what ever your sda is)
cp -a /old-myth /myth
go have a coffee ~ beer ~ glass of water as this will take a few minutes.
When it is done, goto the menu and do a Restore! When finished, reboot.
It should be real close to where you were originally, minus any tweaks. Run it for a while and see if the problems you were having still exist with the new drive. If happy, upgrade to R5C7 and try it out.
But that is just me and my approch
Have a great day!
Mike