As I said, anything following the "index.php" is ignored by the server. It may or may not be ignored by index.php (and I think not; Based on your description, index.php examines the requested URI and acts upon the information that follows "/index.php/").
So, you could either use the code I posted above to redirect all such non-standard URis to index.php with all the trailing info removed, or you could modify index.php itself to look for old-style URis and redirect them, 410-Gone them, or whatever you wish to do with them

You really need to change your product and cart design and theme it plus intergrate it better in to your website. Also you need to make it more prominant on your homepage.

I would use Google Analytics and see where the majority of your visitors are bouncing.

If they are leaving on your homepage, it means they arn't even getting to the products section so you would encourage them to go there by better "advertising" this link on your homepage.

If they are hitting the cart, but bouncing before checkout then you need to make the checkout process better & simpler for them.

etc etc

Just go through your logs and find where you are loosing visitors, and fix this page.