40-50 minutes per log file? Yeah, you should be able to speed that up... (Dependent on hardware of course, but my Mail::Log::Parse modules go through 8-9MB (after compression) logfiles in around a minute per (compressed) megabyte, and they do a lot more work than this.)

The other comments on combining patterns could be useful, but the other thing to look at is what exactly your patterns are. Small differences in patterns can make some fairly major differences in speed. (Of course, if you are doing literals it's probably not that bad.)