After installing the granite, I am now contemplating staining or painting them a different color, perhaps a dark espresso stain OR paint them a beige cream either of which would match the granite.  

The bones were good, little lawn work, paint throughout, and I replaced a scalloped finish on a beam with stained wood and wrapped it.  

Then paint the walls and ceiling.On the cabinets, moldings, I would go with polyshades to stain and polyurethane in one (staining and sealing)..

If the finish on the floors is largely gone and you can see or tell the urine is present there, I think you are a candidate for refinishing them-- rent the sander (use various grit levels) stain/polyurethane. 

I think hardwood stairs are beautiful and carpet gets stained easily.

The easiest things to do are: Exterior painting, Interior painting and staining/sealing the concrete on the first floor.  

What about stained concrete?

Not to mention how stained they left my carpet.

Damaged parts of the property, curb appeal, look for water stains or running water it can signal a big issue.

I didn't have a rust problem, but I see that the product claims to eliminate rust stains.