Getting 100% bootrate after this, coldboot to RxTools emunand every time. I'll probably edit this a few times as i remember things.

First of all, I'm using Ninjhax, I also have a Gateway and Pasta, but all you really need is access to the Homebew Loader.

I zipped up the RxTools Nightly and Boot.3dsx I'm using. Available http://andrewiankidd.co.uk/other/RxToolsHomeMenuHax.7z .

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Pre reqs
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Have access to the homebrew loader, have access to internet.

Backup your SD card

Have the zip I linked extracted to your SD card.
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Setting up unlinked Emunand
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If you have a Gateway card, remove it

Open the o3ds web browser, navigate to http://go.gateway-3ds.com/[2]

You should see the gateway menu, scroll along until you see the Format Emunand option

Activate this option and wait for it to finish, once it's done, reboot without the SD card

Go to settings and format your system, it will need internet access but WONT update, so dont worry.
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Installing HomeMenuHax + RxTools
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Setup Wi-Fi on your 3DS (should be in freshly wiped SYSNAND, hax free)

Go back to the Home Screen and click the upper left settings icon, then choose a theme (even basic red)

Quickly load up your Homebrew Loader (via Ninjhax or whatever) and choose RxTools

Follow the onscreen steps to install RxTools

Reboot

Quickly load up your Homebrew Loader (via Ninjhax or whatever) and choose HomeMenuHax

Follow the onscreen steps to install the exploit

Reboot and hold L (skips HomeMenuHax), go into the 3DS Settings and delete the network settings (so SYSNAND wont update)

Power off the 3DS, remove the SD card and put it in your computer

Rename boot.3dsx to HBL.3dsx (or just delete it), rename bootrx.3dsx to boot.3dsx
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Booting into Emunand
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Put the Sd card back into the 3DS and turn it on, while the system tries to load the theme, it'll trigger the HomeMenuHax exploit, which loads boot.3dsx, which (in this case) calls RxTools, which then autoboots to Emunand.

The first thing you should do is go into Settings and verify that the system version number shows as 'RX-E', that means you've booted into Emunand!

The second thing you should do is change the Emunand theme+layout, so if you ever accidentally boot into sysnand, you'll know. I have a bunch of folders on my Sysnand, that spell out SYSNAND so I never accidentally update.

And lastly
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Injecting CIA installer
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reboot the 3DS (last time!), when all the HomeMenuHax text first pops up on the screen ('Hello'), immediately press and hold L

You should see the RxTools menu, navigate to Advanced, and FBI injection. If you attempt to install it to EMUNAND, it'll tell you some information, region and a number.

In my case the region was eur, and the number was 3077.

On the SD card, I went to E:\fbi_injection\eur\v3077 and moved the two files (fbi_inject.app, fbi_inject.tmd) to the root of the SD card (E:)

Reboot back intot he RxTools menu, and re-attempt to inject FBI, it should work this time, replacing the health and safety app.
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end
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Thats all the steps, seems like a lot but now whenever I turn on my 3DS i'm in a safe emunand environment, without having to load up and wait for gateway or cubic ninja.

video: https://www.youtube.com/watch?v=WzJ0HFT1Z1Q