1. Most of the time it's because a widget's width is too big for the sidebar. You'll need to set the width's yourself in the control panel. Start out with a value of 50% for the content and 25% for the sidebars and keep adjusting until you get the widest content without the widgets overlapping the side.
2. The tagline has a class of .description so you can change your css according to that. If you add this code to the custom css box in the techozoic options page. Then you can play with the values until you get the desired affect.

3. In my new version of Techozoic I have created a dropdown nav menu type. It should be ready in a few days.
4. Also in the new version of Techozoic I have an exclude pages from navigation section where you chose which pages not to show in the standard navigation, then you can edit the footer.php and add the links there.

To exclude pages you'll need to edit whichever nav type you've chosen there is a file in the nav subfolder that has the same name. In the file you see a call to the wp_list_pages function you'll need to edit it to look like this.

Where 1,2,3 is a comma delimited list of page ids. Then for the footer you'll need to add this code to the footer.php file

where 1,2,3 is a comma delimited list of page ids that you would like to include in the list.

Yours is a different issue when you were adding the header flash file since the directions where with a different version there is a extra closing div tag. If you look in the header.php directly beneath your flash file remove one of the closing

tags and you should be good to go.