After the automated process, you have to update the SU binaries by opening the SuperSU app. Then install busybox with the installed app.

That is the next step, but if you do not achieve root SuperSU and busybox will not allow you to install.  I ran thru this procedure 6 or 7 times with no success.

I apologize.  I did not intend to make an ignorant statement.  The problem I am having is this with Version 1.5.4.  I check the root box with custom recovery either checked or unchecked.  The scripts seem to work just fine but at the end when I run SuperSU it shows no apps configured and no logs available and it does not prompt to change the binaries.  When I run Root Checker it says I am not rooted.  That's why I made the ignorant statement. 

I got unrooted when I upgraded to 4.1.2 from 4.1.1 because I had not installed to OTA app that prevents unrooting. 

It was not my intent to offend anyone or diminish the efforts of those who I agree have been helpful.  The reason I made my statement is because the scripts all seemed to work (no errors) yet when I ran SuperSU as prescribed at the end of the scripts it does not prompt me to update the binaries.

In SuperSU settings I have Superuser enabled, Re-authentication and Show notifications checked. v0.96.

I'll got to sing the praises of Lastpass basic is free and $12.00 gets all the extras. It stores in the cloud and on each system you use it on, each blob of password is encrypted so only you have access to it. You can access your passwords via an app or web browser, it will create strong passwords and remember them for you. I love it and it has the Steve Gibson stamp of approval, don't get better than that in my book.
Www.Lastpass.com
Rainman

The only problem I have with Lastpass premier version on the Nexus 7 is it is unstable.  I have to restart it frequently which is a PITA if you have a complicated Lastpass master password.  I use Safe Notes to store the password to copy to Lastpass.  Safe Notes requires a 4 digit PIN so it is easier to use than retyping an involved password.  Safe Notes lets me copy/paste the password to Lastpass.  I have checked the Lastpass support site to fix the stability issue to no avail.  Lastpass does not crash on my iPod Touch or my B&N Color Tablet (gingerbread) so it must be a Jelly Bean issue.

It is still the best password manager IMO.  I will not get the Xmarks ($8) option again though.  It does not play well with the Google Chrome browser.