I would say your knee to wall stretches are irritating your patella. This is due to the weighted forward position your pushing your knee into with that stretch.
You said you've been doing heaps of mobility work. Have you followed Dr. Kelly Starrett at all? Simply typing his name into youtube followed by "ankle" will yield you a dozen or more videos containing multiple mobilizations.
His book Becoming A Supple Leopard is also worth its weight in gold. I too have really poor ankle mobility and many of the techniques I've learned from him have been very helpful. Definitely get to know Starrett if you aren't familiar.
You just have to experiment and see what works for you. Some mobilizations I see little change from, others make huge differences. Also, concerning knee pain. Look into "voodoo flossing" the knee. Makes a huge difference for me.
Here's a link to a 30min mobility class for ankles instructed by another PhD who works with Starrett at his gym.
Best of luck!