If you're an amputee and you haven't flown in a while, this brief video will show you what to expect from both the airline check in and TSA security screening process.
I always choose the millimeter wave scanner. I find it reduces the chance of a pat down. I also wear shorts, it just make it easier for the TSA agents to see my prosthesis and what’s all going one.
That's a really good question. Being a bilateral amputee myself, I've never had to take off my shoes but I'm pretty sure that if you told a TSA officer that you are more stable keeping your shoe on your "sound" foot, they would let you keep it on. Over the years they've become more educated & aware about the needs of the disabled.