When the instructions state that there should be no more than a 4% difference in mosture content between subfloor and the hardwood flooring, does that mean that if the subfloor had a 5% moisture reading, that the hardwood flooring should be no more than 9% or no less than 1 percent, or does it mean that the flooring should be no more than 4.16% or no less than 3.86%?

The former. I'd also check underside of subfloor. It's important to take multiple readings and get averages for the subfloor and flooring.