I don't think there's any cleaning up to be done - as far as I can tell what you describe is what an old SID softmod looks like when it's finished. In fact, any attempts to clean the system up might leave it in an unusable state.....
As for the file renaming, that's how a softmod works - renames the original dash from xboxdash.xbe to something else (msdash.be, or xb0xdash.xbe, or xb1xdash.xbe, depending on the softmod), then adds a replacement file called xboxdash.xbe which is the one that loads the fonts to launch the softmod. I doubt that there are any incorrectly named files on there unless someone changed them manually.
Your Xboxes are probably in different states because you seem to have used different softmods.
To cut to the chase, you currently seem to be running two very old but similar softmods, which have all sorts of odd features (like needing to run Patch 5960), and importantly have lots of features missing, like shadow C, and virtual eeprom. This can lead to all sorts of problems, the biggest of which is that your real C partition is exposed, and hence your Xboxes are vulnerable to having the softmod overwritten. If you are happy then just leave well alone, but the best way to clean them up is to upgrade to a newer, safer softmod with better features (and no need to run Patch 5960!), and if you want to do that then post back and I'll be happy to talk you through the process.
Edited by Heimdall, 24 August 2010 - 04:23 PM.