I recently started a new job as a contract developer, and my non-developer boss of about two weeks ago gave me the task to re-create an app from another language and developer that he will reuse with multiple clients (replacing the front-end), that I estimated would take longer than his estimate of 12 hours.

Two weeks later, I'm 230% over-budget. I admit this was my 2nd web app, I had been a wordpress developer in the past, so I am somewhat new to code igniter, but not shabby php by any means. My boss hired me knowing this and I was clear that it would take longer than his 12 hours. He's seen me in the office on task for 2 weeks, he should be somewhat prepared for this bill.

Do I expect the full amount of hours, or do I filter against how much of learned? Can I bill for research as a developer?