Well, it seems you have enough air compressor volume, no question there. Volume is more important than pressure.
Quote:
"Should I remove the line going to the pump and make sure no water remains in the pump as well?"
You can run the pump until dry, won't hurt it.
"I preferred to handle the fresh water with air so I applied about 55 psi with all facets open."
Actually, it's best to not open all at the same time. Go to the furthest point from the pump first & work backwards.
"Most had a little water come out except the rear master bath sink facet. No water came out but I couldn't hear any air either. Could that be a problem?"
That is strange, especially with that size of compressor. I would start over with the procedure mentioned above.
PS: When using air, there is no need to mess with the water heater by-pass system. The very first step with air is to drain the tank & re-insert the plug & go on from there.