Can’t save down more, than ~90 menu items

This isn’t a limitation of our plugin, our code doesn't even load in your menu manager. It’s a WordPress and server setting problem. The WordPress menu items usually have around 90 item limit, because its PHP by default doesn’t allow forms to submit more than 1000 post variables = ~90 menu items. The solution usually is to increase the max_input_vars to 2000 in the php.ini file in your root folder, like this:

max_input_vars =2000

If you don’t have a php.ini file, then you should contact your server host to increase it for you.