> Before running Clr I had 170 roms fail audit, after I had 397
well...then I'd say your old audit was wrong.

clrmamepro is pretty strict on some aspects of romsets.
I don't think you made anything wrong. If you used the scanner with all check and fix options enabled (which you don't seem to do, otherwise you won't have the "wrong name" or "missing but fixable" messages) you will get a fixed version of your collection against the currently loaded database.
so, 1st thing to check is that you use the correct database, i.e. the MAME version you're using should also be used for auditing. Best thing would be to use your MAME binary in the profiler: Profiler->Create-> ... There is no need to use anything else (like the mentioned rename dat). Keep this binary-based profile and everytime you replace the MAME binary, clrmamepro will detect this new version and regets the data from it.
Secondly, be sure you got all scan, check and fix options enabled. This means: Sets + Roms + Samples + CHDs (ok...samples is a bit optional in this aspect). All check options, name, case, unneeded etc...and the fix options right besides these check-checkboxes.
After a new scan with these options, you should not see your stated "wrong name" etc messages anymore since clrmamepro correctly renames/fixes the files.
Keep in mind, all removed files (due to unneeded check) will be placed in your clrmamepro backup folder.
Now you say that you don't care about *all* sets...well..then of course you will see some missing set information in the scanner tree.
Question is: what do you want to achieve? A complete set? Then keep them showed up and try to get the missing ones. If you're not interested in them, you can hide them.
For hiding there are several options possible: Either use the scanner popup menu->View -> hide completely missing sets, this will hide fully missing sets

Or go to Scanner->Set Information (button on bottom left of the tree window). There you got options to limit the to-be-scanned sets either by manually enabling/disabling them or using lists of sets/regular expressions and so on.
How to add files to your collection: You can put new files in 'add paths' (settings->path selector->addpath) and fix-missing will pick them up or -the prefered method- use the rebuilder to add them. Rebuilder can also be used by drag'n drop operations in the scanner tree window.
Hope this helps a bit for now....documentation hasn't been updated for a while (yeah yeah...real life...)...maybe it also helps if you check out some tutorials here:
http://mamedev.emulab.it/clrmamepro/docs.htm