WRT clipped shoes in transition - at the moment I prefer not to & run barefoot with bike past T-zone and then slip shoes on/mount bike at same time. Its not pretty but works for me and has improved my speed/hassle through the T-zone. Coming in I have my feet out & on top of shoes from 100m or so out and then jump off & run through to change into run shoes. Sometimes I carry my bike on my shoulder as the shoes are so long ( size 13) that they drag on the road otherwise. I have Nike tri shoes with two straps that I use sox with when training but not racing. Part of my brain seems immune to pain when racing....put it down to adrenaline.....although the shoes are not painful, just better with sox if you've got time to worry about such things.
Note - I'm only doing club races here, not anywhere near elite level ( ...yet, he says hopefully....)