Great research. Regardless of the statistical issues you mention, this is a clever way to try to get numbers that automakers don't necessarily make public. I do think that many of these are reading a bit high due to the misclassification you mention, but with further analysis such as sourcing from more resale websites, you could probably come up with more solid data.
A coupe small things jumped out:
- The M6 Gran Coupe went out of production around the middle of last year after MY2018 ended
- The 4 Series Gran Coupe has no manual transmission option, so it isn't altogether fair to lump it in with the coupe
- The Focus RS ended production last year with the rest of the Focus lineup (no 2019 model)
- The ATS-V Coupe is ending production after MY2019
Here's a very recent article (and, from what I can tell - a much higher quality effort than other similar ones I've seen in the past) listing all manual transmission vehicles currently available in the US.
https://www.motortrend.com/news/ever...r-you-can-buy/
Of course, the Corvette and ATS-V will need to come off the list soon, and the 2020 Sonic is also losing the manual option according to GM Authority. The Fiesta needs to be removed too since, as you mention, that ended after MY2019. Furthermore, VW recently announced that they are killing the SportWagen/Alltrack entirely after MY2019. However, it is looking pretty certain that the CT-4 "V+" and CT-5 "V+" will be new additions, and the G80 M3 will also likely need to be put on the list too.