Is he on any anti-biotics? Has he had a culture done? Is he on anything like Metacam?
Headtilt can be distressing and tricky to treat, but, according to the guy I know who has extensively dealt with EC and head tilt, EC does not cause head tilt. If EC has reached the systemic infection stage then it can lower the immune system, so making the bun more prone to a variety of infections-of which an ear infection may be one of them. However, rabbits can get ear infections with no relation to EC at all. Also mites can cause similar symptoms. The problems are generally found in the 'down' ear, so whilst checking both is important, that is the ear to check extensively.
There's been a lot of head tilt threads here recently (as you've probably seen), maybe scroll the first few of these pages, but also use the search function to find out more.