OK did they change the command structure or am just not doing something right?

What commands have you tried? Which version of PEX? Have you read the wiki for 1.x or the getting started guide for 2.x?

/pex group Owner create
/pex user Ironic_8b49 add permissions.*

either one I tried I got error in logs

[22:51:42] [Craft Scheduler Thread - 16/WARN]: Exception in thread "Craft Scheduler Thread - 16" [22:51:42] [Craft Scheduler Thread - 16/WARN]: org.apache.commons.lang.UnhandledException: Plugin Autorank v3.8.2 generated an exception while executing task 29 at org.bukkit.craftbukkit.v1_10_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:56) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.NullPointerException at me.armar.plugins.autorank.permissions.handlers.VaultPermissionsHandler.getPlayerGroups(VaultPermissionsHandler.java:104) at me.armar.plugins.autorank.permissions.PermissionsPluginManager.getPrimaryGroup(PermissionsPluginManager.java:93) at me.armar.plugins.autorank.playerchecker.PlayerChecker.checkPlayer(PlayerChecker.java:54) at me.armar.plugins.autorank.playtimes.PlaytimesUpdate.updateMinutesPlayed(PlaytimesUpdate.java:63) at me.armar.plugins.autorank.playtimes.PlaytimesUpdate.updateMinutesPlayed(PlaytimesUpdate.java:81) at me.armar.plugins.autorank.playtimes.PlaytimesUpdate.run(PlaytimesUpdate.java:30) at org.bukkit.craftbukkit.v1_10_R1.scheduler.CraftTask.run(CraftTask.java:71) at org.bukkit.craftbukkit.v1_10_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:53) ... 3 more

That looks like an error with Autorank, not PEX. You should talk to them about the issue.

Ok there was no change to the commands, Thanks