pex 2.0 not loading on my spigot 1.10.2 server got error in logs:
http://pastebin.com/zdFGMKy1

Got other errors with Essentials-2.x-SNAPSHOT-#13 and EssentialsChat-2.x-SNAPSHOT-#13;
http://pastebin.com/My6gZkg6

since its a fresh install I would not think there was.
http://pastebin.com/vhWrv0EV

Nope, you have made changes to the backends section and it is very wrong. Here's a corrected configuration file:

multiserver:
  use-netevents: true
permissions:
  debug: ture
  allowOps: false
  user-add-groups-last: false
  log-players: false
  createUserRecords: false
  backend: flat
  informplayers:
    changes: false
  basedir: plugins/PermissionsEx
  backends:
    sql:
      type: sql
      url: mysql://mcaaron:MissPiggy69@localhost/pex_minecraft
    flat:
      type: file
      file: permissions.yml
updater: true
alwaysUpdate: false

This configuration file is still in a 1.x format, but it is more correct (note the backends section), so updates can actually happen now.

I must of accidentally copied the config file in pex folder when I was grabbing my permissions.yml file I deleted the one that was there and it loaded up fine, thanks for giving me the format on how to setup the file when I'm ready to set up SQL.. will PEX 2.0 work with the my old permissions.yml file?

PEX 2.x is not for Spigot. It's for Forge/Sponge.

There actually is a build of PEX2.0 for spigot, but it's not really ready for general use yet. It seems like you have an issue with the backend setup in your PEX config as well. To use Essentials, you need to use a recent build of EssentialsX that has been updated to also handle PEX 2.x.

However, at the moment PEX 1.x is still recommended.

I was using permissionsex-bukkit-2.0-SNAPSHOT-shaded-#136 even without essential installed it still wouldn't load

Pastebin your config.yml for PEX, there is an error there.