The accent stone wall can be a beautiful texture to blend with your farmhouse look if done correctly. Here are a few inspiration photos to motivate you to embrace the stone. You could have your island refaced as in photo one or photo two painted in a lighter color as suggested below. Take down wall cabinets and have mirrored back wall for light with gold modern and glass shelving. Update Hardware on cabinets. Create a bar or accent and fun objects. New counter tops as below and I would not do pendant lighting I would do recessed lighting as ceilings are low. Another option to have metal racks on stone wall for wine display. Lighter unified flooring will help as well and have you said which flooring color yet? If so a photo would be helpful. Also, what are you going to be using this space for? What a fun project to work on as you have a wonderful lower level space to work with and good luck.

I don’t know what the average cost for a nice bar cabinet, what the average cost?

Put the doors back on the closet, so it looks a bit less cluttery. Get some brighter colors in there, and and put in night stands, and end tables with lamps on. Use led bulbs in the 4000 range so that you get a feel of daylight in the room. First the bed in place, since you say there is a limited space for it, and then fit the other things in where needed. An area rug that has a bit of color in it, would look nice. Right now, it appears a bit cold and unwelcoming

Huge decisions for entire room and the bookcase should be what connects the space. Since the slate is a given, definitely start there and you‘ll get a much better sense of a direction. One way or another, I don’t suggest white walls, and think big picture vs one decision at a time. Hard to suggest, as your furniture and lighting also play big parts. If keeping the wood, avoid a sharp contrast/work with the slate when painting the upper walls and create a connection by adding a similar shade grasscloth on back of bookcase. Replace hardware and I’d remove the two narrow shelves to create a more modern look. Consider the advantage of painting, as you’ll have more flexibility and a big change would be removing the desk section, if not needed, as well as the cabinets above. Add art/a light and the entire bookcase will be transformed. Next decision is painting the walls or not. Not sure if Railings is complementary with the slate, so consider a touch more blue. Really important to test against the slate and also the wood.