The garage and it's poorly thought out bump up torpedoed the Colonial Revial facade long before the new windows ever did. No decor changes will fix what feels wrong here. It's an architectural issue, not a decor issue. You might as well go with the direction that the home currently trends toward, which is modern, especially since you aren't going to change the windows. I think if you redid the roof as a flat roof and concentrated on "color blocks" and other rectangular and linear shapes, you could manage to pull what's there to the modern side. You could also redo the garage bump up area by making that roofline shorter and smaller and "nest" into the main gable end rather than being on the same plane. Turn the windows into dormers and do the whole addition in a darker color for it to recede from the main box of the house and that would take it back to the more traditional side. You would still need to change the windows to a more traditional muntin look or add muntins to the existing windows.

this product claims to preserve the wood while letting it age naturally. I haven't tried it myself, but have seen buildings done with it. They look nice.

The window trim change would be to Craftsman style. Unless you are doing the work yourself it seems a lot of expense for little difference on upstairs windows. It would, however, be extremely easy to do on your front door as you would only need to change the top board. And you could replace the side lights with solid wood inserts, or you could use textured glass that would obscure the view while still letting light in. While the limestone exterior is very light it has a yellow hue. Simply speaking the easiest way to find colors that work with the warm limestone is to choose a nearby color. That was probably why the trim is green. Since you prefer a modern look, I suggest you keep your siding light and use color only in the trim. Below are two combinations that I like. I darkened the roof color in these pictures.

I wouldn't go so far as redoing the roof - meaning new rafters and support structure, nor sliding the bay window over. Might as well build a second floor if going to that much trouble. First I would pick a consistent color, either the white of the window or off-white of the gable for all trim. Then I think its a matter of differentiating the bay from the gable end - they kind of blend together with the same siding. So like these examples: The middle white one the bay blends in vertically like yours, but its the same color. The blue and beige houses differentiate the bays from above them. So for yours, the eave bracket detailing is rather simple, so you shouldn't do a lot of busyness. Just adding trim to separate the gable, even carrying that as a frieze board across the top. Adding window head trim (maybe as prominent as a crosshead). Adding a water table trim along the bottom (maybe future full watertable of brick or something). I think I would avoid vertical trim on the bay, to accentuate the horizontalness and balance the skinny verticalness of the massing. I show a window as well, same size as the gable window, if that works in plan. Symmetry forced onto a facade is too contrived, just try for balance. For the porch, can't tell what's going on in this pic perspective but maybe you could just extend the roofline as a shed, maybe the same slope if it works.