First step you did was to disable opera's built-in pdf plug-in viewer. That you've done already.
Try this next. Right click on a pdf file. A context menu will open up. My system is windows 7. Select "open with" "choose default program" If you for example have Adobe Reader on your system it many be listed under recommend programs. If not click on the little arrow by "other programs" and select what ever your external pdf viewer is. Next make sure that the "Always use the selected program to open this kind of file" box is checked. Click on "OK" The extension of a pdf file is now associated with this program. So from now on a pdf file should now open in your chosen pdf viewer. Hope this works for you. Good luck.