Sorry, but your work flow is just strange to me.
In the Calibre Editor you can generate the NCX. THEN you can generate the Inline TOC (On the Tools menu)
Once I have a Clean EPUB, I can convert. No need to have conversion insert things like the TOC, scale fonts...
My flow:
Add to Calibre
fix metadata (Library)
Use Polish or Modify EPUB to insert it into book
Use the EPUB Editor (or Sigil) to tweak the code
Generate/replace the NCX
Optional: Generate/Replace or Remove the inline TOC (I onlyAdd if converting for my K4)