I was just reading that Hydrogen Peroxide, Baking Soda and Vinegar are all ammonia neutralizers.

You also want to set the tone & precedent from Day 1.Definitely try to find out if there are any major electrical/plumbing/roof issues, but other than major mechanical items, I would not ask too broad a question.On the shower head, often it is just some calcium build-up inside the showerhead, and simply placing the shower head in vinegar for several hours will do the trick. 

I always find it better to work with honey then vinegar.

I tried everything to fix the odor (scented oil warmers; baking soda on the carpet then vacuum; vinegar), but finally had to tear out the carpet (did it myself).

The other contractors simply say: "will spray with vinegar and paint the ceiling (kilz and then regular paint).

Honey, not vinegar. 

I've cleaned the ceramic tile floors twice - once with bleach and once with vinegar solution, but the smell is still there. 

Asset companies ask them to pay for trash outs and winterizing and get re-imbursed and sometimes stiff them on the payouts.Investors eventually learn they catch more deals with honey than they do with vinegar.

But I'm worried that it will show stains like wine, lemon or vinegar.

1) You can get the hardwater stains out by draining the toilet, then fill it with white vinegar and let it soak.