Is there a particular movement(s) or position(s) within the programming which is causing the flare ups?
A new or different movement during the times of the flare ups?
Or an increased number of reps of a movement?
Is your arch collapsing?
What is going on to cause the achillies issues?
The cause may be outside of your training time– environmental loads.
Changes in other parts of the day?
Changes in work shoes from the prior pair?
Are you warming up/cooling down with workouts.
Nutrition — decrease in eating connective tissue within diet? This happens with eating leaner meats or not on the bone. The connective tissue has key amino acids which are large components of the collagen& collagen matrix that make up the health of a tendon.
Have you been taking antibiotics?

Good to hear you are working up/down stream of where you see the issue.
Have you addressed the ankle and/or hip joint capsule?
Pro Episode # 21 – Pro-User Request Friday: Not Seeing The Change? You Need a Systems Approach.

Can you have someone ball whack the area for you?
Tuesday, October 31st, 2017 – Ball Whacking & Gua Sha

Good to hear you are seeing ROM improvements with your right ankle.

Gastrocnemius and Soleus are the main sources of power for the motion of the ankle. When the calf is tight the ankle is not able to move properly. The connective tissue of these muscles form the achillies tendon at the back of the ankle. They are interconnected when one is tight the other is tight. With sore or tight muscles our movement is different. Concentric motion (going from standing to tip toe) is impacted.

The soles of your workout shoes may not show much, however, the inside are worn out if they are a year old.

Sounds like your calves are asking for attention.
What are you doing to desensitize the painful area?
A Leopard Claw or HawkGrips work great or if you have another tool is one way to desensitize the area.
This will help to feel less distress and shock in the tender area(s). Gradually exposing this area to more aggressive work is more effective. You want a dose and a response.

In the beginning, 2 shorter (5:00 or so) sessions may be needed. Manageable doses is key to being consistent with working on tender areas. Daily doses start to normalize the tissue.