How do I adb pull (backup) root directories (like "/" or "/system"?)

Hi there, I'm trying to pull root directories like /system and /data without any luck. My purpose it to have them on my PC as a backup, and be able to browse them to pull out apps and pieces of data as necessary if it ever becomes necessary.

Device: Nexus 6P (North American version)
ROM: Stock 6.0.1 Rooted, using Wugfresh Nexus Root Toolkit and SuperSU
PC OS: Windows 7 PC (64 bit)

Adb is working properly and I can easily pull non-root directories like "/sdcard" and so on. I'd like to be able to backup the entire root directory ("/") or at least the child directories (like "/system" and "/data", etc.) Unfortunately, when I try

Code (Text):

1. adb pull -p "/system" "C:\somewhere"

it skips a bunch of files, so I need to come up with a better method.

I've tried

Code (Text):

1. adb root

and it tells me it's already running in root mode.

I try

Code (Text):

1. adb remount

and it does this properly, but doesn't change the effects of all the commands I've tried.

When I run

Code (Text):

1. adb shell

it enters shell and gives me # by default, so seemingly it is giving me su permission by default?

*** Oddly, when I enter "su" while in shell, it tells me "/sbin/sh: su: not found" which seems odd to me. I think it's possibly that SuperSU is installed as systemless root, or there's something else screwy here, so I guess I'm not sure how to proceed. Still, if that were case, why would adb already be running as root, and why would shell automatically give me the #?

Any help is appreciated!!

Thanks!