Hi M;
As I understand it, I don't think your plan will do what you are hoping. (I could be wrong)
If part of your plan is to insulate the whole building, what I suggest is an 8" batch box with a brick bell.
I would cut registers into the floor upstairs to allow free movement of the heat, and fans of course as well.
Rocket mass heaters are moving away from the J-Tube design with pipes thru a solid mass, to a Batch Box design with a hollow "bell" (bells are commonly brick but can be metal lined with brick or covered by cob or brick)
Your shop will be warmer than the upstairs, but as heat rises the whole building will be very comfy.
It would be nice if your chimney went straight up rather than a double 90 out the wall but what you have is completely usable.
Here is a link to Peter Bergs Batch Box site to learn all about them.
https://batchrocket.eu/en/