[Nexus 6 Android Development] Woody:
Here comes my installation with Viper, Android Pay, Layers, SuperSU and many ThemeReady version of Google Apps.

First, this worked for me. If it works for you then great. If not, you need to put in some elbow work and see where it goes wrong; this includes multiple backups and reboots if applicable.

What I did in order was the following (Screenshots posted below-where applicable).

6 Jan Stable - In Aroma, I unchecked nearly all Google Apps. In fact the only ones I left checked were Gmail, Plus and Hangouts. The rest I installed from the Play Store.

Flashed ElementalX

Flashed UnSU by [MENTION=4544860]osm0sis[/MENTION] (This guy is the bomb. I have seen him on several different devices that I have used in the past and he is top shelf. If anything and even if they mean nothing in the real world, hit his Thanks button. He's put in the work so you don't have to.)

Got back to TWRP main screen and then went to Advanced>Terminal and typed in (minus the quotes) "echo SYSTEMLESS=true>>/data/.supersu"; Hit Enter

Flashed SuperSU 2.64 (the only reason I flashed this and not 2.65 or 2.66 was because I forgot to download those)

Booted up and went through setup process

Restored Cataclysm Settings

Opened Market and installed Root Explorer and Titanium Backup

Used Root Explorer and deleted the xbin_bind folder from the /su folder and Rebooted.

Once booted up, installed Android Pay from the Play Store (I did not install it at initial flash in Aroma).

Added my card(s) and successfully passed the system check.

Made a backup with working everything right there.

Once I rebooted, I then manually pushed my Layers.apks into /system/vendor/overlay (*Pro-Tip: If you have a layer setup that you like, put a folder on your SD Card labeled "My Layers" and then copy all the apks from /system/vendor/overlay into it. That way if your Overlay folder gets nuked for some reason, all you have to do is create it and copy them right back in. Been doing it this way for a long time.)

Pay still worked, so I made a quick backup of system and proceeded to test the ThemeReady apps.

While I was waiting for a working version of Viper to come around, I was at a fork of what to test. So, from that point on I tested the ThemeReady apks built by the most fantastic themers [MENTION=2126467]djdarkknight96[/MENTION] [MENTION=5476501]Train88[/MENTION] [MENTION=4603975]daveyannihilation[/MENTION]

Davey worked up some serious magic and created an Aroma Installer, which was invaluable for testing something like this. I tested each one of these below in individual flashes and verified that Android Pay worked after each boot. If it is not listed below, that is because I don't use it. Note: I did not flash the Contacts and Dialer, as I barely use my phone for a phone and there were other more important things to test.

Gmail 5.9.109452737

Google App 5.7.14.19

Google Plus 6.9.0.109819508

Hangouts 6.1.109448852

Play Store 6.0.5

YouTube 10.49.59

Edit: Clear and Black YouTube from TBO work as well

While that was happening, I had a few people send me a "working" Viper zip. Believe it or not, the only one that worked for me was the original AIO-Viper.zip from way back when. Either the install would break Pay or the driver would cut out in under 15 seconds.

As I said, this is what has worked for me. I have Layers working, all my normal apps, full Root, Pay and my music to drown out anything that is driving me nuts while at work. Big thanks to my friend [MENTION=5244502]micmars[/MENTION]

Edit: In reference to the question below, I don't use Xposed at all. You can test if you want. Good luck though.