I haven't time to read your detailed report.
All I would comment is, if you think it is wrong, it probably is.
If you have seen it and don't like it, your eyes will be drawn to the areas in question forever.
That said, very often (and likely) any remedial works to brickwork or stone may very well end up looking far worse than what you have now.
At the end of the day only you can decide.
If I or anyone else said you were being picky, would you then accept what you have?