You may want to find a chiropractor who does extremity adjusting and see if there are any fixations that can be adjusted out.
Ankle flexion mobility drills. See this article
for some, Z-Health is also a great place to learn them from. There are some YouTube videos on basic mobility drills, some of them are on this page
You may already have done or are doing some of the above. If so, you may be stuck with a problem that isn't the end of the world. Simply keep squatting in shoes--better to squat than not!