My family and I have remodeled over a dozen older homes. Most of the time “creepy” feelings have a very real world cause.
First things first – I’ve had bats, mice, birds, squirrels, and raccoons in the walls/attic/soffit space of various homes. Check soffit vents, attic vents, chimney caps, and the roof ridge line for animal access. Exterminate as appropriate. This is my first suspicion if it’s upsetting your dog–they know what’s up.
Next, prune trees and shrubs from rubbing against the side and roof of the house.
In a basement room, throw windows open wide and thoroughly flush the air for 20 minutes every other month to let the radon out. We can’t really smell or detect problems with radon, carbon monoxide, lack of oxygen so get an “off” feeling from our lizard brain.
Then I would check for airflow, heating and cooling issues. Check for blocked air ducts, clogged cold air return filters, flush radiator lines, etc. All of these can make noise, cause vibrations, make weird airflow, “coldspots”, etc… Check windows for missing or deteriorated weather stripping.
Check electrical fittings. smell for burning wires. Did someone put a nail through the wires in the wall? Did mice chew all the coating off? Electric wires have a magnetic field and can make the hair on your arms stand up especially when improperly encased–they can also smell like ozone (its that “dry” smell after lightning).
Check for gas lines, possible gas leaks.
More difficult to diagnose are low frequency vibrations. It could be the whole house sways in the wind. It could be road noise vibrating the upstairs window differently that lower windows protected by shrubs or fences. One house I lived in, the siding would groan as it heated and cooled.
It could also be that the upstairs has been a liminal space you haven’t truly “lived” in. Liminal spaces always have a weird energy. I suggest spending time up there and decorating. Definitely turn on music, radio, or tv to mark the space as yours.
So, once you have eliminated all of these; most “presences” feel a lot scarier than they are. Fresh paint/wall paper/new flooring tends to make the place unfamiliar to the “presence” and they leave on their own. I’ve also simply instructed them that they were no longer welcome and to get out.