I can't believe most of your questions aren't answerable by a search. However:
1 - Yes you need to replace all rubber between your high pressure pump and fuel pressure regulator with new EFI hose. You may aswell replace the rest of the rubber too, but you can use cheaper non-EFI fuel hose for this. The metal sections will work fine still for EFI.
2 - I can't see why you'll have any problem with extractors unless they physically hit your alternator. If there is a problem just make a new alt bracket, or move it somewhere convenient. I've seen them work fine both high and low mounted on 4A's
Interesting that your using all the old 4AC accessories, different to normal, but it should work, just bolt it all up and see.