[Sony Xperia Z Ultra] SUPERUSER:
You downloaded the SONY EMMA flashtool. Not the one we need.

The name is a bit confusing because they are called the same.

The flashtool we need is this one. Download it via torrent its the fastest way.

http://www.flashtool.net/downloads.php

Uninstall Emma and install this flashtool.

...time for some ugly doodling

When you are done installing flashtool and are met with the UI you will see a main window as in image one. Press this button on the far right with the XF logo.

A new window will open with the name XperiFirm as in image two. Scroll down the list on the far left until you see the Togari.

Select your device. In my case I have the C6833. Now go to the list in in the middle. Click the "check all" button to fetch all updates.

When this is finished you will see a the latest "version number" on every "operator" in the collumn to the right.

Click the stock rom you would like to download in the list that correspond to where you live.

I always download customized DE because it includes the region I live in. Now look at the list to the right.

A list will appear under the "Available Firmware:". Click on the one you want to download. In this case there is only one entry.

Almost all older stock rom has been removed lately so it is very rare that you will find any old based on jelly bean or kitkat.

Anyway. When you click the one you want to download a new window will open as shown in image three

You will see some info. Double check the name is the one you want to download. If its right. Click download and make a coup of coffee.

When the download is finished you can close the window and let flashtool do its job. When its done.

You can see it in the log when it says its finished.

Now you want to press the button all the way to the left. That thunderbolt icon as shown in image four

A new window will open. Select flashmode and press ok as shown in image five

A new window will open and here you can see a list of which stock roms you have downloaded as shown in image six

Select the one you want to flash and look to the right in the "Exclude:" box. Make sure nothing is ticked.

And press flash when you are ready. And follow the instructions following by flashtool when it is ready.

Optional

If your phone is not detected in flashmode you need to install S1 - flashmode driver. You can do so by follow these steps.

Go to this folder as shown here in image seven

Execute the file as shown here in image eight

Select Flashmode Drivers as shown in image nine You don't need to select fastboot drivers. Because you already have this working.

If you want you can scroll down and select Xperia Z Ultra drivers as shown in image ten however this seems to fail in Windows due to driver signature verification.

Its not necessary to select it. Click install and hopefully the device will be seen when connected in flashmode.

For zip files. What you find here on the forum. You flash these in recovery. Not very difficult. You can find loads of guide on how to get started learning how to use recovery mode.

.img files. You flash via fastboot with cmd. Not very difficult either. Key tip here is to don't make typos or you need to rewrite the whole command again..which get boring fast.