Please help with some layout issues with css and swf

I am having trouble getting my customized wordpress theme to layout properly. I started out with the template called notepad chaos, which had several “position:absolute;”s in it, which were being weird, so I started to change them to “margin-left:auto;margin-right:auto;padding-right:20px;” or whatever to bump it into place. That is causing problems, as well as the swf that I placed Here are the main problems:

Here is the link:
http://saulojulio.com/thebreadshack.com/

1.The swf file I placed into the header using Kimili Flash Embed has a mysterious space around it, which is not in the original swf. It only seems to appear once inserted into the wordpress site. It looks like it is making the swf document size bigger than it is. I have checked the publishing settings in flash, and when I publish it and view it, it is showing the specified size which is 789×240. But on the worpress site it is showing up with maybe 30px space on both size and a 10px on the top and bottom.

2. In the browsers that I am using, there seems to be an extra, empty div appearing below the header. The swf is within div #container, and then an extra div #container is appearing below it empty. I am sure this has something to do with the flash, but I don’t know how to fix it.

3. Basic layout stuff: Since I changed the css from absolute to margins and padding, I am unable to get a few things back into place, such as: the search bar is meant to be next to “search” in the header, now it is below the header; the date tabs are meant to be farther to the left, overlapping the brown frame, and not inside the content; and the footer text is meant to be over the brown paper in the footer, and the rss button over the bottom right corner of same. I am considering just going back to the absolutes, and dealing with it, but I know that they are not encouraged.

Any help and/or advice would be greatly appreciated, as I am self taught, and don’t have anyone to turn to over here. This is my first time using WordPress, and I am enjoying the challenge. I am excited to move on from the design so that I can experiment with all of the potential that wordpress has to offer. Please know that your help will be appreciated. thanks