Mike,
Great to hear you are looking at environmental factors that can impact mobility and your experiences in life.
1% better in an aspect each day translates into solid sustainable change.

The ankles can be stubborn.
Have you check out this episode?
Pro Episode # 44: The Last 25% of Your Ankle Restriction (Snatches and Pistols here we come!)

Excellent to hear you are feeling great.
Sounds like you are building a good understanding of concepts.
It is ok to use Oly shoes with squats. This is one application for oly shoes.
However,continue working on your ankle restrictions.

You can mix in working different areas as you are working with the ankle restrictions.
Can start another archetype or if an area needs attention.

Spending 10, 20, 30 minutes a day helps to stay on top of things.
Some days you may have more time than other days which is fine. Consistency in getting a dose in is key.

Great results with what you are doing to address the ankle restrictions. Chipping away at it.