The house wrap(Tyvec/etc.) will eliminate a lot of the air holes. That will block a lot of the wind by itself. The R value of the foam board is in the 3-4R range. It does not replace wall cavity insulation, but adds to it and also helps seal air leaks. What Bill said about the baseboards/electrical is true. However, house wrap when properly installed can solve a lot of those issues. I am all for preserving the look of old houses, but houses built in the 1800's and into the first half of the 1900's were not built with any energy conservation/effeciency in mind at all. Plus, many of the materials used were all that was available and needed periodic maintenance. Those are now expensive and uncomfortable houses in which to live without extensive upgrading. I remember a house in which i lived when I was young. Even then I loved the big front porch, the screened sleeping porch(with a huge feather bed). But, it was cold in the winter, we had to have individual heaters in the rooms we used the most, and hotter than all get out in the summer. Our present house was built in 1965 and was upgraded with insulated steel and insulated plastic(looks like cedar shake shingles) siding. Still has the original windows, but has two piece storms over the windows. I added more insulation in the attic and we can relax in below zero weather in summer sleep wear.

Shadygrove is right about not using a solvent on asphalt shingles. I would however be a little concerned about shingles glued down that were not woven into the installed roof, might create a catchment that would hold water and cause problems. And the irregularity might be more obvious than you would like. Replacing one or several shingles without compromising the integrity of a roof is not difficult. Google "shingle repair" and you will find any number of pages showing how it is done with everyday tools. I did this recently to cover a roof patch where I had removed a chimney, and there was nothing technically challenging about it at all. The trickiest part was not sliding off the 5/12 pitch roof. Since your roof is new you should be able to buy matching new shingles, but if not just swap out the painted ones for some others from an inconspicuous part of the roof.

Seems to me that painting over the white with black paint would be the easiest way to deal with it. I wouldn't want to try removing the white paint as you could end up somehow compromising the shingles' effectiveness (scraping, etc.) and why work that hard if you can just go over it?

@bry911 thanks for responding. Found myself here while searching for ways to remove subfloor all the way to joists and build back up with new decking. I don’t plan to remove subfloor under exterior walls or the one interior wall in this space. Just inspect and replace everything necessary. I realized after moving in that the house was vacant for 15 years, bought and flipped. Roof has probably had several leaks for a long time, leading to a few surprises. I’m handy, but Im not a contractor, having to figure this out as I go. Whatever I do I want to make sure I don’t cut corners, or compromise the home in any way. Problem, 66’ home with cold floors, soft and sinking in a few locations. Vinyl flooring over subfloor and 10” joists, 24” on center, 4 foot tall crawl space, 3-5mil plastic vapor barrier (not taped or sealed to foundation wall) on ground. I’d like to strengthen up the floor, apply closed cell spray foam under the entire floor and put back up the bat insulation. If it’s going to cost $10,000 I simply can’t do it, I’ll have to patch fix and deal with it. If I can find a way to do it for cost of materials and a day laborer for a day or two, might be possible. Just one of multiple projects, backyard grading isn’t ideal either, have to tackle that too. :/. Wish there was a homeowners anonymous group I could come to, help others with their problems, potentially get help with mine.