Hello Jeff. What exactly is the issue? Sounds like you know exactly what needs to be done.
For point number 4, as you say it’s not necessary, if you’re the only one that will be using the model and it’s not part of a big pipeline or anything, you can work a bit out of the ordinary and it’s ok.
And for point 3 and 5, I think the way JL does customs rotations in this video will help you out with that one, it’s around 17:53
https://cgcookie.com/lessons/modeling-the-left-leg-i
