Before when someone had problems uploading a logo, it was due to a plugin they had…I cannot remember what plugin it was but it was affecting the customizer upload function (which incidentally is a WordPress function and not a theme). So here are a few tests for you….
1. disable all plugins that you installed and then try the logo upload
2. For the font plugin, try it with the default WP theme such as twenty thirteen and see if it works.
When you say production server, do you mean for developing your site? IS this off your host’s server or local as on your computer?