This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
This is a forum to help provide pointers to learn Java, so you're unlikely to find someone willing to simply review hundreds of lines of source code in multiple files so that they can do your homework for you. To get help here, or on any forum, distill your question to its simplest form, post the minimum amount of code needed to fully express your question, and keep your questions focused. In short, ShowSomeEffort. At a minimum, ask a question. Your post simply said "I need it to work." A worthy goal, to be sure, but hard to define.
Based on the one file I did inspect, you're using a JSP to do *everything*, from database setup to conversion to writing to the new database. This is bad practice; you should be using JSPs for presentation and delegating your business logic (i.e., the tasks of uploading files, converting them, writing to databases, etc) to separate, specialized classes. This allows you to break problems into common parts and reuse solutions in multiple locations, rather than recoding everything from scratch each time.
Best of luck on your project. If you have specific questions, do the work and put together a question here and I'm sure we'll jump on it--this community seems very eager to help out people who want to help themselves.