Just had a similar problem after upgrading to 1.1.6.
For me there was at least one missing file after the upgrade:
(that one was causing a missing setLocation error)
I downloaded the full zip of 1.1.6, extracted it and copied the file in place, and now no more setLocation error at least, and the pager is working again. Hallelujah!
Also js/varien/iehover-fix.js was giving me problems in IE 6 after the upgrade, so at the moment of my writing, I have it disabled by commenting out its loading in layout/page.xml (not sure if it’s related to the fact that js.js has been missing since I upgraded - need to re-test).