I had this problem a long time ago when I mistakenly chose the System 9 version of Adobe (Acrobat Reader) when in a browser window to open a PDF. Forever after that became the default for the browser(s).
After some time I came across MisFox which solved the problem.
http://mac.clauss-net.de/misfox/
I see there's a new version which is now a Pref Pane, I had used an earlier version which was an App.
Let us know if it helps.