OK, so the search engines cannot read any of the content embeded in flash… so you have 2 options:
1. do away with the flash and create a contextually rich site with strong landing pages focused towards your targeted keywords. Embed some flash if you really want, but try not embed too much of your copy to any of the flash. I would not recommend replacing any of your headers or links with flash either and of course, make good use of the noembed tag.
2. If you really need to keep the flash due to the nature of the business then create a second HTML only version, text and links only which will never be seen by human beings, but only the search engine spiders. Essentially you will be cloaking your Flash site from the spiders and visa-versa for your human visitors. Search engines do not have a problem with cloaking as such, so long as the content of the cloaked content is the same as the content seen by humans. Use a list of IP addresses for all the search engine’s locations and (if you are using apache) use your .HTACCESS file to redirect the search engine IPs to the text only version.