Okay I've got it working now and updated the plugin. Download this plugin again and replace the old one, it may require some testing still but so far it seems to work with no problems. Active Item System Developer mode works too.
Follow these steps:
Highlighted in this image with a red square around it is the symbols you need to enter into the Mano_InputConfig plugin. These are case sensitive.
once you have the info above place it into the Mano_InputConfig plugin for the appropriate gamepad button like this:
You can also set the following to show the proper text in the menus for each button. You can go with whatever Text you wish to display, I chose to go with 'Toggle+' 'Toggle-' and 'Use Item'. Whatever you type in there is what will be displayed in your gamepad/keyboard config menus.
I've tested this with keyboard and also with my gamepad and the buttons work for both.
(If you're curious as to what the problem was, the compatibility fix for yanfly keyboard config plugin I made was conflicting with the Mano_InputConfig plugin you're using because at the very bottom of Mano_InputConfig he sets Imported.YEP_KeyboardConfig = true; which made my plugin think you're using Yanfly Keyboard Config so it will try to modify some of the Yanfly Keyboard Config plugin that doesn't exist. I added a catch to avoid touching that code if my plugin detects Mano_InputConfig.)
Thank you for choosing this plugin and I hope this solves your problems! If anything else comes up be sure to let me know.