What do the paint colors look like? I'm not familiar with SW since I only use Behr paints. Certain shades of gray look great with natural wood. I painted my foyer and living room with Classic Silver from Behr and it looks great with everything. I personally prefer gray paints over beige. I just checked out your colors and to me, they look very similar, especially on my computer monitor. The gray is not what I call a true gray. Here is what I have on my walls:

You have a beautiful home. I would recommend going with a light gray/beige color like the picture I attached. Yes, paint the ceilings but an even lighter shade than your walls.

A picture or two of the actual walls you want to paint will be helpful. The cabinets show very yellowish on my iPad and I suspect they aren’t.

He needs a new twin bed for sure and as for wall color keep it neutral since his favorite color will change many times over the next few years. That dresser in front of the wall heater needs to be moved , it is always best to have nothing in front of a window that kids can climb on and maybe just put that in the closet. I think the wall color you have works well Get some fun removeable decals all about dinosaurs BTW all 3.5 yr boys love dinosaurs and I love the bedding. A littl bean bag in a gree for a spot for him to sit and could you show the whole room , IMO he needs books