I have a new server and only OP can do everything successfully. When I DeOP myself I get a message that I don't have permission. I don't know what I'm missing here. I'm trying to keep it simple for better troubleshooting. Here's what I have in place.

CURRENT PLUGINS:
NoSwear
Essentials
Factions
MassiveCore
PermissionsEx
SimplifiedSpawns

CURRENT PERMISSIONS.YML FILE
schema-version: 1
groups:
Member:
default: true
permissions:
- modifyworld.*
- essentials.home
- essentials.warp
- essentials.warps.*

I've tried with - essentials.home and without the dash now as above. Neither makes a difference. I tested code in http://yaml-online-parser.appspot.com/ to make sure code is without errors.
What am I doing wrong here? I'm prepared to wipe all plugins and start over if necessary.

Sounds more like a permission issue rather than an issue with EssentialsX

Yes it is, sine OP has no issue using Essentials commands. But I have problems using permissions to do anything. I've seen many videos and samples but I must by typing something wrong and I have no idea. For whatever reason I copied and pasted this again and rebooted the server and /home works now but warp doesn't. I guess I just need to keep playing with it since no one on any forum can seem to help and they all just point fingers at least other.

Not an issue with essentials. Sounds like not having permissions configured correctly.

Yes you are correct. Strangely after all the advice I've seen online saying "4 spaces to indent, no tabs" it turns out 4 spaces is incorrect. I had to use 2 spaces and everything started working. Not sure why my permissions.yml needed 2 spaces to indent each section when everyone else says 4 spaces, but that was the solution for me. Thought I'd share incase anyone else having the same problem.