3) I highly recommend the new composite pre-hung doors with integral threshold similar to the Endura Framesaver. The bottom 8-12″ of these frames are made of composite wood guaranteed for life against termites and rot. Check out their videos. I also suggest using composite or PVC door brick moldings and a pre-made sloped sill pan.
4) Dylan Chalk is an ASHI Certified Home iInspector and ASHI Western Washington Chapter member. He is the owner of Orca Inspection Services, LLC and president of Quality Inspection Reports, LLC. Check out his excellent article on why doors leak.