What material is your exterior? Will you be able to "match" the material when you raise the window? You might also consider making it wider. (That might also provide you with material to patch below the window if, for example, your exterior is brick.) Here are some pictures of counter-height windows. Of particular interest are MamaDadaPaige's window and ErikaNH's window. Scroll down to see both the interior and exterior. Note that the exterior frame might be used to alter the exterior if you cannot match the current material. Thread: counter height window pictures please https://ths.gardenweb.com/discussions/2484108/counter-height-window-pictures-please

The whole point of stone countertops was that one would never have to replace them. "They will last forever" everyone claimed, to justify their use. Those stone slabs were quarried from the earth and transported via ship from a quarry that is not likely to have been in North America. Do you really want to refresh by putting them in a landfill? I would, instead, stick with more easily changed colors and trim. I like the color of your maple cabinets, too. I fear that darkening them to the color of the beams would make the kitchen feel much heavier and maybe oppressively so. I would keep the cabinets, paint the peninsula some (taupe?) color that goes better with the travertine, but pairs well with the counters. If the backsplash really does not look right (can't really tell without a view of the tops of the counters), then replace that. Just be careful to choose something that is not trendy - or choose something that is a cutting edge thing that might yet become trendy - or you will be wanting to tear it out in five years. With cutting edge, you may get ten. If you really want to replace stone counters, try using Formica or Wilsonart, so that it is far easier to change them out when you become tired of them.

Not a continuation of the grammar and punctuation sidenote, but some verbage in the OP to me could be interpreted differently: is only the Breakfast Room the addition over a crawl space, but the Kitchen next to it is unbearably cold, or does the Kitchen extend into this crawl space addition? And, could this crawl space be an original part of the house, say a porch with stone piers, and they captured the space? Or, is it a newer CMU addition next to the old stone basement foundation? Also, your description of "remove HVAC ducts and plywood for insulators" might say something: I'm picturing your ductwork is hanging below the floor joists in a vented crawlspace, and probably uninsulated duct? Only 1 or two ducts for both rooms, and were the runs taken off an existing furnace? Is the bottom of floor joists covered in plywood for some reason? If it were my house, I would first understand the construction and areas of improvement for insulation and air sealing, then review HVAC. If the entire house is forced air, including the Kitchen and Breakfast, I certainly would not introduce baseboard heating of any sort. Nor electric radiant for such a large area (keep it confined to bathroom tile in a forced air house). And, if it were a forever home of high market value, I would review whether I could dig the crawlspace a bit deeper (your description is "small and crowded" but if contractors don't like it that would say to me there is no headroom) and simulataneously work on a mud slab/radon/encapsulation all at once. FWIW: HVAC is any method of Heating Ventilating Air Conditioning, you have forced air. And vented crawlspaces have been and are still to code - that is the cheaper route than an "unvented" and conditioned crawlspace.

Update: The wall with the windows has been primed and I've narrowed down some colors. They are in the same order along side each cabinet. There is an additional color added in the under cabinet lineup. I’m having a hard time deciding. Do any of these work or should I do something else? I'd love to hear your feedback!