Yes we have to add the links through the files can you please send us the site url and the login details to support@flythemes.net so we can add your links to the icons.
You can add the icons to the services boxes and all the icons are coming from the font awesome so if you want to add other icons you need to add the name of that icon in icon parameter in the shortcode.
For adjusting speed in free version open custom.js file in js folder of your theme directory where you can see the nivo slider function at the bottom where you can change the speed.
The slider in our theme is an image slider where you can add the title, content and the link but the pop up video in slider is not available in our theme you just have to add the link for the slider. As per your requirement you need to use any plugin.
