It sounds like you have MC set to write the content of MC fields to the file tags. If so, begin with deleting all unwanted file tags/MC fields in MC. Select all files and in the tag action window, set to show all tags with values, empty the tags you want to delete. Then you can remove the MC fields in the settings.
Thereafter you can use MP3Tag to find and delete the rest of the unwanted tags:
In settings make sure read all tag versions is set for mpeg and that write only the tag version and charset you prefer is set (ID3v2.3 and ISO charset, for example) and that delete is set to delete all tag versions EXCEPT the one you prefer. EDIT: Attached a screenshot to illustrate.
Load all files into the program, select them all, and choose save (this will ensure you have your preferred tag version written to the files)
Then, while all files are still selected, choose delete tag (and you should only have the preferred tag version in your file tags; embedded cover art is in my experience not affected)
Now, while all files are still selected, choose the Extended tag panel. There you can see what tags are in your files. Just choose delete for the ones you want to delete and click OK
As a precaution, if the fields in MC are as you want them and set to write to file tags, select all files in MC and choose update tags from library.
You may want to try this out first on some test files.
There is unfortunately nothing you can do about MC writing unnecessary Tool info to your file tags.
