If you get a new disk with similar geometry, then the next time the system goes down, install the disk. Then, when you have time, do a dd (disk to disk) copy and competely mirror the root disk unto the new disk. (or do this just before a reboot). Afterwards, swap the new disk (freshly made with dd), with the original root disk. If you do this at 'targets of opportunities' when either down or rebooting, then the transition to an error-free disk can be made without being too intrusive.
I'm sorry I'm not much more help on the disk error. They make me nervous and I see them as a warning sign for future failures. My apologies for disk-paranoia

About the error in your pkgtool distro, you might try just copying the entire directory with cp -rP (or something like that) and then move the old directory to an archive; then move the tree made with cp -rP (or whatever works for your system) back. You might get lucky and the disk error will remain in the archive tree and the new tree will be error free. This is a shot in the dark, but sometimes these wild-arse-guesses get lucky and solve obscure problems.