Please post some common examples of the file names and locations that can't be scanned.
If these are permissions or password issues, the simple answer is no, there is nothing you can do if you the user haven't got permission to access an area (short of running the scan from a user account who has permission).
Well by default the .log/.txt files aren't scanned (as they are in effect inert), unless you have gone into paranoid settings, bumping up Sensitivity to High, Test whole files, etc. etc. as that could have the impact on performance you mention delay in opening large files, more so when you add scan for PUPs also.