I wouldn't worry about the duplicate application. Most companies won't really get worked up about an extra copy of a resume for a candidate they liked.
The recruiter situation is a little tricky, but I wouldn't worry about it too much. It's important to remember that the recruiter doesn't work for you, they get paid for filling Job Orders. Think of them a little like a car salesman. You don't actually owe them anything, but it's a good practice to deal politely and honestly with everyone.
In your situation you've already given him two weeks, if they still don't responded it's likely that the company already passed on your resume and the recruiter didn't care enough to bother telling you. It's rude, but when you get paid per placement time is money and manners often get dropped. You should definitely still reapply with your referral, because having that real person to vouch for your skills might make the difference.