For all at once? By clean you mean....... trim?
I would trim all of them down to something between 5 and 10 thousand lines all in one shot, with a shell script that simply opens each, copies output to /tmp or something, and then back to /usr/local/apache/domlogs...........
Is this the type of thing you mean? If so I could help further with specifics....
You'd be restarting apache afterwards of course.