"Which still leaves us rising and lowering on three and. So if I read this correctly. Three starts with the foot half way to closed. That would give us a big three wouldn't it."
Maybe not as big as you think. Step three likely ends when the heels touch the floor, but there is a lot of lowering still to do after that, which would be part of the following step one.
Similarly, in the music step three's halfway closed beginning likely occurs around the "and" BEFORE beat three, and ends fairly shortly after beat three. Much of the "and" after beat three would belong to the next step one, as that is the time in which the movement of leg and body would have to be in progress if that next next step one is going to strike on beat one.
If you wish to subdivide the measure and action each into six pieces, you are going to have to put carefully thought into exactly how they line up, in ways in which you did not when you danced them as 123. And you probably will not find what you like when you look at that.
I would instead strongly recommend that you forget about counting at all. Learn to create a properly sequenced natural turn action without any music. And then learn to fit that whole thing as a unit to the entire measure as a unit. Don't worry about precisly what part matches what part, because you won't like the truth when you discover it. Instead, have the body's energy match the energy of the music.
And for foxtrot that is going to be the only way to make it work, as the true detailed relationships are far too messy to try to write out formally.