And you DID do the file repairs just prior to doing the in-place upgrade?

I guess trying an earlier restore you might get back to a place where the files are undamaged but then you 'll have to be on guard about what damaged the files and try to avoid that. More frequent images could be insurance against that. Other than that, yes a clean install is a possibly better solution, but only if the cause of your disk damage doesn't recur plus you have to do the extra work of reinstalling all your programs.