I agree with what everyone else has said. I think they've caught the obvious stuff. Now, to keep going, can you post the execution plan from the query, preferably after you fix the functions that are preventing index use. That can help to figure out if you have good indexes in place and they're getting used properly.
"The credit belongs to the man who is actually in the arena, whose face is marred by dust and sweat and blood"
- Theodore Roosevelt
Author of:
SQL Server Execution Plans
SQL Server Query Performance Tuning