I am using the current version of manjaro xfce. I was attempting to use the auto injectu wad v 3 program with wine. Of course, it did not work. Do you guy know any programs that do the same as auto injectu wad and customizMii for Linux
I can't help you with similar tools for injecting WADs for Linux (since i use Windows OS and my tools i code are for Windows), but i could help you with this another alternative: using a "virtual machine" (VM).
Did you try using a VM (Virtual Machine) running on Windows like Oracle VM VirtualBox
It's avaliable for Windows, Mac OS and Linux.
Here you can download VirtualBox for your Linux OS (Ubuntu, Fedora, Debian, etc.): https://www.virtualbox.org/wiki/Linux_Downloads
Now the next step is making and installing a VM for run Windows (I recommend Windows 7 x64 bits, but you can use Windows Vista, 8, 8.1 or 10 as well). On the internet there are tutorials
for installing Windows in a virtual machine on VirtualBox, just google it.
Once you have installed the Windows OS in your VM, download and install the required plugins for run the tools (to your Windows VM of course).
But before doing this... can you tell me what Linux distribution (OS) are you using?