It should not be painful.
If it feels sketchy it is sketchy so go to something different.
It may be beneficial to start with a softer ball.
I would recommend getting one of the Yoga Tune Up options:
Therapy Ball
https://www.yogatuneup.com/ytu-therapy-balls-wtote  
OR
Therapy Plus Ball
https://www.yogatuneup.com/therapy-ball-plus-pair-tote
You can use both in the mesh tote they come in to replace the 2 lacrosse balls taped together.
Do 10-15 a day.
This can be before or after a workout or at a completely different time of the day.
Did I over do it?
From the FAQ
Only you can answer that question. The MobilityWod program has often
been described as self-inflicted torture. But, don’t be foolish – if you
think you are injuring yourself, STOP. Don’t over do it. More is not
necessarily better.

I broke my shoulder blade and collar bone on the same side at the same time.
I have no pain, restriction on movement, and no rom limitations.
Establishing improved positioning with your shoulders and t spine may help address the pain that you are experiencing.
Clear the T-Spine, Now We Can Start Talking Shoulders
Basic T-Spine Mobilization
T-Spine Plate Smash
T-Spine Smash – Double Lacrosse Ball
T-Spine Overhead Barbell Smash
A Better Upper Back Extension-izer
Pro Episode # 9 – Spinal Archetypes
Episode 283: Resetting After a Shoulder Tweak/Brutally Sore Shoulders
Episode 199: A Word About Your Shoulder Health
Pro Episode # 40 – Pro user Request Friday: Spinal Rotation and Forward Head