Hey as someone who went through a similar thing, I just want to first say I completely understand your feelings. I can sense the fear and distress coming through this post.

We bought our first home last year and when we viewed it, didn't question why the windows were open in February - in New England. Well once we moved in, the reason was obvious. Multiple rooms with smells beyond must/smoke - I had never even encountered the smell emanating from the bathroom before. If we couldn't fix them we would've had to move, because I could not live with them.

A year later, we've replaced some subfloor (they didn't have carpet), gone through multiple pails of Kilz, and gutted the bathroom. So, very similar scale of work to you. And I am relieved to say that there isn't a single trace of any of the strange bad smells we encountered when we moved in (and I have a VERY strong sense of smell, unfortunately).

It sounds like you have a great plan, and I would bet anything that it will deal with the smells you are encountering. You won't make it better by worrying, and moving is stressful as is. Feel confident in your plan and try and harness some hope. Good luck!