Can I clone a drive from a spanned volume?

You may end up cloning the errors as well. An imaging program capable of handling all four drives at once like the Acronis True Image server edition would be able to handle Dynamic volumes if that's what you are working with there.

The best time for any imaging however is while everything is working 100% to make your backup of the entire setup just in case something like this comes up. The imaging program used would back up each block to be restored on the new identical replacement drive in order to work.

The manual method of copy and paste or creating a separate backup where you can pick and choose the new and unreplacable items would be the first suggestion since those options wouldn't include any errors as for the C volume only any files found fragmented in their present condition.

Besides a main image to get the OS or in this case a spanned OS volume backed up you may want to make separate incremental backups for the additional items as you go along in case something like this comes up again. And to back anything up you are going to need at least one or two other drives that are not part of the WHS set up in order to store them separately.

It can be a real pain at times but the manual copy and paste insures a good copy of each and everything you want to keep is safe elsewhere. You would be doing the same with any data recovery program only face the program possibly renaming things during the recovery process. At least you can pick and choose what to C&P over what can simply be redownloaded again with a quick visit to each site.

Try looking at about 1,000 numbered folders when a drive on an older XP system was recovered and even the individual files were given a number instead of preserving the file names! I prefer manually copying a 358gb folder over to another drive and watch as that seems to take forever rather then going through the process of not only reinstalling but "resaving" things like gave saves for games and where I left off with other projects.

You want to know what's even more fun?! Try backing up entire folders manually from a dos prompt! That was long before backup options were available for the old Legacy days!