[Nexus 7 (2013) Q&A] MrAwesome75:
Well, I am no expert on any of this. I've just gained a little experience on rooting and flashing over the last year and a half. My advice is to watch a lot of You Tube videos and read a lot of articles and XDA posts to get familiar with all the steps involved before you do anything.

At least we know that if your Nexus boots, it's not broken and you will be able to root it. The only thing I was unable to do before I found this thread was use a custom recovery, but other than that the tablet worked fine and was rooted.

That being said, I can kind of tell you the steps I took, but in no way, can I take responsibility since I am admitting that I really don't know what I'm doing, I have just been able to follow the guides that I have read and watched. Also, I am not going to get extremely detailed in the steps. There are a few different steps and you can find much better guides than what I can give you.

I just did this whole process again on my brother's tablet:

1. The first thing you need to do is unlock the bootloader. That is simple using ADB or the WugFresh tool. (There are a few minor steps that need to be taken before you can even connect to the computer, but I am assuming you know about USB debugging and "Developer Options" etc.)

2. Next I Rooted the tablet using CF-AutoRoot. That is also extremely simple; basically a one-click process.

I flashed the modified TWRP before I rooted and then flashed the regular TWRP with Flashify afterward, but that didn't work for some reason.

3. Soooo... I went back to ADB and flashed the modified TWRP again. That seemed to do the trick, but I have no idea why since I am just a monkey tapping keys. I am not sure why this makes a difference since when I did it on my tablet, it seemed to work fine the first way (unless I am just not remembering correctly).

4. I would suggest flashing the normal recovery next (TWRP, CWM, etc). I assume you could use ADB for this (I don't know for sure), but I used Flashify since that was suggested on the OP for this step. Flashify is a free app you can download from the play store and flash recoveries and other files. I would suggest doing a search and reading up and watching video tutorials before using it. It's super easy, but if you flash the wrong type of file you could have issues.

5. I then re-flashed the modified TWRP from the OP. This was done with ADB.

Once the phone booted back up, I went into recovery to make sure it worked. Like the OP says, in TWRP you can tap the small square at the bottom, middle of the screen (in the recovery home screen interface) and if you don't get a screen full a RED errors it worked and you're good to install ROMs and make back-ups, etc. If you do get errors (like I did the first time I did this tonight), do it again. When I got the errors tonight, all I had to do was re-flash the modified recovery file from the OP right over the tablet without wiping anything and I was fine. It's possible that you may have to wipe and restore and do this process again, but it depends on what your results are. Wiping, is never a bad idea when you have problems, since it gives you a clean slate to start with and can sometimes save you hours of frustration, but flashing the file was fast and easy, so you could try it first and see if it works. Although, if you follow these steps and not make the mistakes I made, you might be fine and be done with this process in about 30 minutes or less. Even with the problems I had tonight it took less than an hour to go from a brand-new in the box Nexus 7 with 5.0 installed to CyanogenMod 12.1 running 5.1.1.

6. At this point you may loose root. Just plug it back into the computer and run CF-AutoRoot again.

You should be good to go. I hope this helps. If you need help with the more technical aspects of some of the specific steps just do a search on XDA or You Tube.

Enjoy!