Keep working with rebuilding your feet.
It may take some time, but you will be in a better place.
Yes, you can do skipping in bare feet. You don’t want to do too much too fast barefoot.
Have someone video you doing the movements where you see the issue so you can see exactly what is going on.
Continuing to work with you hip mobility will help to improve your position when landing.
Have you looked at your ankle range of motion? This may be a contributing factor.