Hello,

I'm wondering if we are able to purchase a licence that would allow us to modify the index.php and various css stylesheets of MJ so we can customize it our website?

You can modify php files because of they are licensed under GPL. But I'd recommend you to rename template in this case so that you can safely update MobileJoomla without overwriting your changes.

As to css, all our templates load css/custom.css file (if it exists and not empty) where you can override any css rule. And this file is not overwritten when you update MobileJoomla.