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So, I have an existing site that is run on Joomla. However, I'm not getting the SEO results that I would like to get from the site. I want to create my own HTML and then have links into different pages so clients can get to the content that is managed by joomla. So, with that being said, I have multiple questions:

1) How do I bypass index.php and it not affect the joomla install
2) How do I get all of the existing links from the index.php file and link them properly
3) Will this affect anything long term w/ my joomla install
4) Has anyone attempted this with regards to SEO and seen positive results?

Thanks in advance!

Why not just adapt index.php to match your SEO requirements?

Short answer to your questions is that you can't. Let us know what SEO results you are trying to achieve and we can certainly suggest how to get them, without breaking Joomla. Out of the box, joomla is extremely good in SEO terms, I doubt very much that any improvements could be made by circumventing index.php.