Build into the time during the day you wear Vibrams. Your foot will be doing the work vs the shoe making the correction. Work with the Rebuilding Your Feet exercises.

You don’t want to do too much too fast. You want your foot maintaining an arch while you are wearing the Vibrams. No reinforcing bad movement patterns with a collapsed foot. There can be upstream compensations from the collapsed foot at the base of support.

Wearing shoes with arch support when running is ok. You are rebuilding the strength in your feet and this can take time. Transitioning your running sneakers is another aspect you’ll need to take a look at. Check out Power, Speed, Endurance for more on this.

Squatting with your feet at an angle you are missing internal rotation at the hip.

There are episodes which address knee pain with squatting. You can do a search on the types of pages.

Not sure what you mean by “I regular CrossFit shoes by Nordic for sqautting.”