Jamie,
I found the issue was I was using SEO with no filename, and the documentation for the mod rewrite, which I did not realize does not show you to use content
Once I added that in it started working. Did not even think about that section until i went to basic, and it worked and worked forward (I actually forgot I did the mod rewrite as it was a couple of weeks ago)
Code:
Setup Instructions Using Mod_Rewrite
Mod_Rewrite is a feature built into Apache web servers that allows you to transform the URL requested by a client into a different URL without the client seeing their URL change in their browser. With this method, when the customer requests a URL like:
http://www.example.com/products/coffee-table
Mod_Rewrite will change their request to include your storefront page without changing the URL in their browser:
http://www.example.com/store.php/products/coffee-table
1. Follow the instructions above in the section titled Setting up SEO URLs
2. Create a blank file with the name .htaccess in the same folder that contains your storefront page.
3. Using a text editor, paste the following code into your blank .htaccess file:
RewriteEngine On
RewriteRule ^(products|categories|news|reviews|testimonials)/?(.*)$ store.php/$1/$2 [L]
4. If you've renamed your storefront page from it's default name of store.php, change that string from "store.php" to your actual storefront page name.
5. Save the file
6. Try loading your storefront page in a browser to confirm that your .htaccess file is not causing any errors. If you receive an Internal Server error, you either have a typo in your htaccess file OR your server doesn't support mod_rewrite. If you believe the problem is the latter, stop here and try the instructions further down labeled "Instructions Using ForceType/SetHandler".
7. Try loading the following URL (changing the domain name in the example to match yours):
http://www.example.com/products/
If you receive a page looking like your storefront page but with a red 404 error in the center, then the process worked. The 404 error appears because you aren't linking to a specific category. If you receive an Internal Server Error, your server probably doesn't support mod_rewrite - stop here and try the instructions below for ForceType/SetHandler.
8. Now that you have your .htaccess file configured and working properly, you just need to tell Squirrelcart to remove the storefront page from the URLs that it generates. To do this, check the No Filename field on your Store Settings page, in the section labeled SEO URLs and click the "save changes" button.
9. You're done! Head to your storefront page and click your product and category links to make sure they are working OK.