Well, before I got to the punch line (of the Krylon fiasco, of which more later), I was thinking in Star Trek terms, as in, "to boldly go where no man has gone before." I have found with my own passenger car detailing efforts that it is impossible to replicate machine-made accuracy, even by using machine-made parts. I have never even contemplated changing a body shell configuration using a pro-level CNC facility. But, as I have said before, I am not devoted to to prototypical window placements; I make do with what I have and design the interiors to fit. Your efforts are several orders of magnitude above what I, or as far as I am aware anyone else, has done.
Also, when I saw the bare metal shell you had, I wondered whether I could ever bring myself to paint it as opposed to leaving it in a polished state. But then I do not have anything in 18" cars that I could pair something like that.
The precision machining in this case is a total relevation to me, as is the availability of the shell you worked on. I might re-think what I have on the drawing board in consequence.
Paint: I haven't had this kind of disaster in a while, but I am generally not painting whole extrusions as opposed to individual parts. I do know that Krylon formula have changed over recent times and as a result the risk of laying down incompatible paint coats is not small. I generally stick with the same brand (mostly Tru Color and Alclad) for all phases of a particular paint application.
In your position I'd strip the shell and even do the filling of the new sections over again to remedy what's happened.
However, chemical stripping may add something to the chemical mix that will cause trouble down the line. I have looked at sandblasting as an alternative for removing paint from metal finishes. Think about what custom car painters do and you will get my drift.
None of that detracts from your effort. I am, as always with your projects, totally impressed!
