The Autoptimize plugin will combine the GP files you mentioned into one file.
Pingdom is only mentioning those files because of the query strings (?ver=1.4.1) at the end of the files.
The Query Strings section of that post shows you how to remove those.
I don’t deny something is going on with your sites, however I find it hard to point the finger at GP when there’s 40,000 active installs and no one else is mentioning an issue like this.
Once the query strings are removed, Pingdom will no longer mention those files, which are just CSS files – they won’t slow down your website (at least noticeably).
Waiting 3 minutes for the Dashboard to load (GP doesn’t load anything in your Dashboard) isn’t normal, and doesn’t have anything to do with a theme (GP or any other theme).
Install this plugin: https://wordpress.org/plugins/query-monitor/
It will give you a better idea of what’s going on – whether it’s a plugin, your WordPress installation or GP – I’m more than happy to help you get it sorted.