Hi After Midnight Games,
I'm glad to hear the Independent Items plugin is working well for your project!
1. Removing the quantity menu
The quantity window is pretty integral to the Limited Inventory plugin, so fully removing it isn't straightforward out of the box. You might be able to get close to what you want by combining my Item Actions plugin with the Faster Deposit/Withdraw plugin. The Faster Deposit/Withdraw plugin lets you deposit items with Shift + click, which could streamline things for you.
Please note that both of these plugins are exclusive to dmplugins.com and require a commercial license for access. Here are the links for your convenience:
Item Actions Plugin
Faster Deposit Withdraw Plugin
If you try those plugins and still need the quantity window disabled entirely, I'd be happy to take a look. Just email me at support@dmplugins.com after you've tested them, and I'll see what I can do to help.
2. Setting slots per item
Yes, you can absolutely do this. I recommend checking the help file since it covers this in detail. You can use the following notetag to make an item take up zero slots:
<itemWeight:0>
This sets the item's weight to 0, so it won't occupy a slot regardless of whether you have the plugin set to "Item Weight" or "Slot Based" mode in the parameters. It should work with both systems.
Please let me know if you have any other questions, and thanks again for using my plugins in your project!