How long did it take you to learn to use your mouse with your left hand? That sounds handy.
I currently get around window confusion by programming the F keys to certain windows. E.g. if I hit ctrl-shift-f1, my currently focused window will be bound to f1. If I hit f1, that window will be brought to the top. I did this with xbindkeys and xdotool.
So when I first start a session, I bind everything. F1 my IDE, F2 my command line, F3 my notes, F4 my browser.
It took about two weeks of daily use. I switched my mouse at work to be left handed and committed myself to not switching back if I got frustrated. Before I knew it, it felt as natural as my other hand, and I can go back and forth with ease. I'd actually say that off-hand mousing is now my preferred state. It helped that at the time I was doing a lot of work in Adobe Illustrator so I was really getting a lot of fine-control practice. You might try playing a game like Minesweeper for a similar effect.
I currently get around window confusion by programming the F keys to certain windows. E.g. if I hit ctrl-shift-f1, my currently focused window will be bound to f1. If I hit f1, that window will be brought to the top. I did this with xbindkeys and xdotool.
So when I first start a session, I bind everything. F1 my IDE, F2 my command line, F3 my notes, F4 my browser.