Sorry – I had it ready this week but could not send it to you. Pls see the attached files in my next message – incorporate them into your site to see the pagination on the shortcodes. You can view the changes by using a tool like DiffMerge or the WinMerge.
I am not sure this needs to be part of the regular theme. Will preserve it though in case someone needs it. The loop-pagination.php change will probably go into the regular build for next update since I see no issues with it.