[Nexus 6 Android Development] Woody:
So this hasn't been my first rodeo and I have been around the block more times than your friend's promiscuous, teenaged sister. To put it nicely, I do consider myself an expert at flashing ALL TEH THINGs.

Open and read if you want, skip if you don't

One of the fundamental things that you are supposed to learn when flashing devices is to make a Nandroid. I know that [MENTION=5964313]wrongway213[/MENTION] just said that he doesn't. This is both good and bad. As long as you have some sort of back up tool, like Titanium or Helium, then no worries. Many of us recklessly flash things and think that "since this is a Nexus, I can get back". Welp, that is true and I include myself in with those rapscallions. Some of these newer users, and with the recent price drop there will be a large amount of them (that's how I got here), may not be as savvy as the likes of the veterans around the neighborhood. Doing the dirty is cool. I have two kids because of it. But when it comes to flashing phones, if you have problems it may be time to wipe and flash before we have redundant questions popping up.

Case in point. I downloaded the update and made a Nandroid right there. I rebooted into recovery and flashed it like I was in a Central Park bathroom in the 1970s. Booted up. Yay!!! Then I flashed my ThemeReady Apps that I test for TBO. Booted up. Yay!!! So for now, everything is as it should be. I then realize that I forgot to flash Viper, so I do. It booted up and a few seconds later I get a notification that my System Storage is low and also a notification that I can clear up some space by deleting SMS messages. Crap!!! All the while my wife is texting me. So I have my wife sending me texts, I am in a conversation with [MENTION=5244502]micmars[/MENTION] about something unrelated and I have these two notifications glaring at me. What do I do? (I have about 40gbs of internal and around 900mb of /system spaces available)

I tried it all. But you know what I did before I tried them? I restored that Nandroid I made earlier this morning. Reflashed ROM and booted up. Notifs. Restored. Wiped system and flashed ROM. Notifs. Restored. Wiped system and caches and flashed ROM. Notifs. Wiped system and said screw this, I'm going to run a batch backup in TiBu and do a clean flash. Did the batch and decided that I need to delete the ROM and try a redownload. So I did. I'm at work now and have no access to fastboot, so this was solely on my phone and no access to my PC for another 6 hours.

Restored once more and flashed the ROM and kernel and let it boot up. Once it did, I saw the "Optimizing Apps" toast go from 1-144 in under 4 seconds. Thought to myself, "Here we go again". Once it finished, I got the home screen and it rebooted again. This time when it rebooted and began the "Optimizing Apps" toast, it took the normal amount of time. Put in my layers apks and Soft Booted. Booted fine. Rebooted to recovery and flashed Viper first this time. It had to re-optimize all the apps again. I then installed the driver and rebooted. No storage error notification. Decided that I would go for the gusto and finish the setup. Rebooted to recovery and flashed all my ThemeReady apps that I'm testing and lo and behold, I got a good flash and boot.

So why the long post? Because even though I do consider myself an expert, poo-poo happens to us all. You need to realize that in order to troubleshoot properly, you need to boil it down to the minimal parts and make sure that each and every one works as intended. Obviously my situation was probably worst case scenario, but by doing it this way, I was able to determine that I did in-fact have a bad download and no matter how many times I flashed it, it was bunk (md5s are for busters:silly:). I had to redownload and take small steps to insure that what I was doing was proper and effective.

tl;dr - Take your time, work slowly if you have issues, clean flash if need be, but above all make a Nandroid, cause you never know when there will be a Ghost in the Machine.