You'll want to look at this document http://www.mojoportal.com/site-search-overview.aspx
because there are some new features like search results highlighting that are disabled by default for backward compatibility with existing indexes, but if rebuilding you might as well enable them.
Make sure you uploaded the new versions of files in the /Setup/ProviderConfig/indexbuilders folder.
Upload those again.
Then delete any existing rows in mp_IndexingQueue and mp_TaskQueue.
Then recycle the app.
Hope it helps,