Do you have an iLok2 new one and registered it at ilok.com?
Also, the AVID Virtual instruments are compatible with PT11. The one that still os not compatible is the PTIEP and thats a separate purchase of 600-700 usd so the intruments and plugin installer AIR Virtua Instrument that you have got with pro tools 11 contains plugins and instruments for use in PT11.
I suspect something else is wrong rather than the fact that you need a secondary harddrive. What installers have you put in the trash and ilok2? Registered? Have you trashed preferences, plists and all that described here after installing PT11?
http://duc.avid.com/showthread.php?t=300050
We need this info to be able to do anything for you.
Christopher