I would leave the ceiling beams in their current wood tone, but paint out all the other trim and doors in the house. Also, find a more contemporary ceiling fan, if you even need it.

Paint the vinyl the color of your wood trim. This is a low price fix. A more expensive choice would be Marvin fiberglass Elevate with interior wood trim. You would stain and finish that. Here. . Now I'm going to suggest something a good carpenter might do. Because your windows aren't opening and are picture the glass could be replaced with insulated units and butyl. This would match your other windows and cost less than vinyl. There are glass companies capable of supplying this. Not window companies. Windows aren't something magic.

if she wants stain, the old finish has to be removed. applying a new finish on top of an old finish will not yield good results. And dying wood, well that has to have raw wood w/no finish at all. I've done it. The aniline dye is water based. It actually absorbs into the wood, dyeing it. And that's where the labor comes into play. sanding or stripping off the old finish. There's no way around it. If you want a new stain color, the old stain/clear coat has to be removed. period. (unless you want a crap job. in that case, just fine sand and rub on a darker gel stain color. ) That's why I mentioned priming and painting. less labor costs btw, most painters don't specialize in wood finishing. That's a whole other skill set. They may employ wood finishers, but most run-of-the-mill house painters aren't wood finishers.

Again to be clear, I was the one who made the window and color scheme selections early-on as I had to choose a whole-house scheme in order to settle on frame/sash colors so that we could order windows. The "third" architect was/is an assistant to the one who designed our house and was my primary consultant in finalizing the siding and trim colors (and hence the original dilemma and possible rescue of the color scheme). I had no expectations of this house looking historic and would have considered a structure of this size and simple architecture to be boring and monolithic were it all the same color. Perhaps I should have asked for help at an earlier point than I did but I do not transfer "blame" (if the word even applies) to anyone else for however the color scheme turns out. If nothing else I can always return to my original plan of having different trim colors on the upper and lower levels, which I didn't think looked that bad. Here is a screenshot I was able to save of the front elevation with all-green trim: