Permalinks change issue

Ok, so, when I setup this website ( site ) I did not set the permalinks to a ‘pretty’ structure (ie. %name% or %post_name% ) and now I’d like to.

The problem is when I go to update the permalinks to a nice structure, it breaks my nav links etc. For example, when you click on ‘events’ it currently takes you to /?page_id=3 with the ‘nice’ permalinks, it goes to /events and gives me a ‘file not found’ error.

I tried the permalinks migration plugin, no joy, I updated my .htaccess file manually, no joy.

What do I need to do to fix this?