Try this. If I didn't mess anything up, it should remove any extra tag without mangling line-endings and thus the md5 checksum of the file (which would be bad).
(Please attach the prettyversion_cleanup.log file that'll end up in the root of your Kindle afterwards, just to make sure everything's ok
)
It *should* at least cleanup the version tag, thus making official updates succeed. However, if the original hack didn't use the same naming scheme as clarknova's, you may end up whith a few *extra* files laying around in the system. (It shouldn't cause any problem, but it's not ideal).
So, it'd be great if you could still find the original hack you used in order to properly remove all traces of it.