When selecting the color, I verifed that the RGB matches up for each settlement, then wrote those values down, then I created the new regions in Japan. Then I selected border regions with the color selector, floodfilled the old regions individually to enlarge existing regions (absorbed into the other regions). None had ports, but of course had the settlement site, which I painted over that sole pixel as well.
Then in each of the three new regions in Japan, I placed a single pixel for the port using the color picker to set the precise value, then did the same for the correct RGB value for the settlement, filling precisely one pixel. Now what I didn't do is assign in the descr_strat the new regions's settlements since I don't know the precise show_cursorstat coordinate. How do you get that value from GIMP? GIMP will tell you the coordinates along the X and Y axis, so there must be a formula to then alter that into something the descr_strat can interpret.
It would be wonderful to get Geomod to work instead for all of the placement issues, but that seems to be very difficult. While both Bare Geomod is very easy and a huge time saver, and Geomod straight forward and intuitive, more times than not you cannot simply open an existing mod with Geomod. It's more for starting from scratch as a tool. It's easy to make a mistake when placing specific RGB single pixel values, and that why I used flood fill to avoid painting issues with a brush.