SO I figured it out! The issue is with the preference.json. 

Once I start Ubooquity.jar it creates all the needed file but for some weird ass reason it will not allow to access anything. I shut it down and edited the preference.json to reflect a (below) path to where books live and restarted it.  I was able to access everything. I've also attached my ubooquity.service if anyones interest for it to startup on start

 "booksPaths" : [ {
    "pathString" : "/path/to/where/Books _ Magazines",
    "userName" : [ ]
  }, {
    "pathString" : "/path/to/where/Books _ Ebook",
    "userName" : [ ]
  } ],
"users" : [ ],

*** ubooquity.service***

[Unit]
Description=Ubooquity
After=network.target

[Service]
User=yourusername
WorkingDirectory=/opt/ubooquity2
ExecStart=/usr/bin/java -jar Ubooquity.jar --remoteadmin
Restart=always

[Install]
WantedBy=multi-user.target

So I kinda gave up on the beta so I waited for the final hoping I wouldn't get the same error. But guess what?

Sorry, you are not authorized to access any file on this server

I've used /var/www/html/uboouity ~/ubooquity and much more with no luck. I'm at a loss here

OK - Now i've tried an completely fresh install of ubuntu 16.04 and I use this command to start 

java -jar Ubooquity.jar or sudo java -jar Ubooquity.jar in my home directory. Still get the same above error.  

java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)