So before I put these back in, what is a good way to really clean and flush these as good as possible?

 

 

air is a popular choice. Id only blow air through the line though, take off the brass block so nothing gets blown into it.

non chlorinated break clean and then follow it up by air

Are you going to add the hill holder system while you are doing it?

nope

ac system blow out and compressed air you should be able to get the blow out stuff at a shop

Alcohol is the only approved brake system cleaner. "Brake clean" is a degreaser for drums and rotors, and not meant to be inside the braking system.