As qwerm excellently put, something to note (that I personally found out as being a bit odd) is that multiple extractors on one root won't speed up the process. One extractor fill at a time.
With 2 extractors rather than come back and find 5/5 as if they work concurrently - you're more likely to see 10/0 or 8/2 - more extractors is like a buffer - I'd say 2 is optimal per root since a full load of 20 will fill your refinery (assuming you have the soft tissue).

I have built everything new and upgraded it all with just two extractors and one refinery. Seems well balanced as each Mistlands area I explored only had about 4 mines holding about 10 Black cores - just enough to build the essentials - And as I finished exploring the 2nd area I've just about finished all the gear. My advice - get the featherfall cape first! :)