Firstly (as Ken, sort of, asked).... the important setting in your config.php file is $CFG->dataroot. Make very sure that this points to the correct place and was NOT changed during the upgrade. Make sure the directory it points to has not been changed or moved.
Failing that, enable Debugging. Try to access a PDF. Are there any additional errors shown? Check your web server's error log for more errors?
Is it just PDF files or *any* file?
If you upload a *new* PDF file, does that work or not?
Failing that, enable Debugging. Try to access a PDF. Are there any additional errors shown? Check your web server's error log for more errors?
Is it just PDF files or *any* file?
If you upload a *new* PDF file, does that work or not?