I don't understand the augmentations system. Please help.

Here's the problem:

OK, so I researched some augmentations. Nice. Apparently it isn't necessary to develop them separately since they immediately appeared as options in my gun development screen. OK, nice. I put several of them on one of my guns in the development process and used it for a time.

Now, I liked one of those augmentations quite a bit and some time later, as I needed a better gun, I wanted to put the same augmentation on another gun. I had researched this augmentation so it should be available, right? Well....no. It didn't appear in the gun development screen any more, and I couldn't re-research it since it was already marked as researched, but since augmentations aren't developed like other stuff I couldn't create a second instance there either?

WTF????

Is this game telling me that researched augmentations are strictly one-time items? In the sense that once used on one gun, I can never make a second gun use the same augmentation? I could understand this if I found stuff, but this was a researched item. Yes, I do know about the different augmentation slots and that they're grouped so that you can use one of each group on the same gun, within certain additional restrictions of which I haven't been able to make sense. This is different. It makes no sense at all, and not being able to craft the gun I want in spite of having done all the research and drowning in resources, that sucks. 

Did I overlook something or is the system designed to annoy me like that?

Oh, and while I'm at it - how do I configure the powers I have available (standard PC controls)? The tutorial showed me but it's so long ago that I forgot, and the control options screens don't mention it.