Don't worry, at least you got all the right files for it to run. I've seen lots of submissions that haven't even done that.
The trick is to build into a separate folder, outside of the project root. Then you can zip that folder up and upload just that. It's strange that Unity doesn't make it clearer all the things you need to do to actually distribute a project.
Don't give up, you'll get there! You did great just to make a finished game in two days.