A script like the one you mentioned would be a huge turn off for visitors. Most people are not going to turn off their blockers, they will simply hit the back button and find another site to go to.
They have their uses, some of the plugins would take months, possibly even years to figure out and code. So instead of recoding them, why not take some functional code and use it. It cuts a lot of time off of the development process.
All of your data is preserved, you may have a problem with the widgets. Some of the themes do not support widgets in the sidebar. There are tutorials out there to add widgets to a theme if you happen to find a theme that you like that does not suport widgets. Change out your themes, hack them a bit until you find something you absolutely love. That is one of the main benefits of using wordpress over a lot of the other CMS's out there.
Very nice! I would suggest a small margin at the top of the page, and a slightly larger margin on the sides. Other than that it looks incredible, better than 99% of the wordpress sites that I have seen.