Kustom is not able to show missed notification counts.

If you want to display a count for other notifications you will have to use Tasker:

“Tasker is an application for Android which performs Tasks (sets of Actions) based on Contexts (application, time, date, location, event, gesture) in user-defined Profiles, or in clickable or timer home screen widgets.” (http://tasker.dinglisch.net/)

If are more interested in Tasker, maybe some guides are a good start:
1. Tasker Tour
2. Beginner Guide by Pocketables.com

I will use Whatsapp notifications as an example here.

This will basically be the same stuff as in Show counter for notifications in Zooper with Tasker variables. If you already have set up Profiles and Tasks for Zooper it will be easier to add Kustom to your setup like in:  UCCW and Zooper counter in one Tasker Profile.

In Tasker I first created a new Project and named it "Kustom". You don't need to do this, because it's simply for a better organization inside Tasker of you have to many Profiles and Tasks (no pictures here, just long press on the project bar and then click "add").

To start you have to create a Task that tells Tasker what to do when Whatsapp receives new messages. To do so go to TASKS, press the "+" and name your task. I called it “newWapp”, but the name is completely up to you. Then press the check mark.

This Task has two things to do. First there has to be a Variable that counts notifications and this Variable has to be transmitted to Kustom.

Your are now in the Task Edit screen and the next step is to add the first Action to the Task. Therefore, press “+” at the bottom and choose “Variables”.

Now press “Variable Add” and name your variable.

Use capital letters because it is a global variable. I named my Variable "%WACOUNT", again this is a free choice. Value is “+1″ because every time a new notification is received one is added to the value . Confirm with the back button.

You are back to the Task edit screen, now you have to add the second Action. Press “+” at the bottom and choose “Plugin”. 

Choose “Kustom LWP” and then “Edit”.

Now enter your Variable from the counting action in the Tasker Variable field and name your Kustom Variable (this will be the name inside Kustom). Press the check mark and confirm with the back button on the next screen.

Your Task should look like mine in the next picture. Confirm with the back button.

Now you need to create a Task that tells Tasker to reset the variable to 0 when Whatsapp is opened. Otherwise the variable/count would always increase. I named it “EmptyWA”.

Now in the Task Edit screen, press “+” at the bottom and choose “Variables”.

Press “Variable Set” and then press the Variable Picker.

Now pick your counter Variable and set the value to "0". Then confirm with the back button.

You are back to the Task edit screen, press “+” at the bottom to add the transfer action, choose “Plugin” and “Kustom LWP”.

Now press Cofiguration edit and then put in your variables as before.

Confirm with the back button and you can see your finished Task. Again confirm with the back button.

Now Tasker knows what to do, but not when. You need to create 2 profiles! “Missed Whatsapp” should be triggered when a Whatsapp message is received and “Empty Whatsapp” when Whatsapp is opened. Go to PROFILES and press “+”.

Choose “Event” in the menu and then "UI".

Then press "Notification" and in the next screen go to the Owner Application picker.

Choose Whatsapp and confirm with the back button.

Assign “NewWA” as the task. For a better look you can rename the Profile to "Missed Whatsapp", to do so long press on the Profile and then "A".

Afterwards your profile looks like this and now you can create the second Profile. Press "+" and "Application" as the trigger.

Select Whatsapp, confirm with the back button and then assign "EmptyWA" as the Task.

 Again, you can rename your Profile.

Your Profiles should look like this and you are done with the Tasker setup.

If you don't want to do this yourself you can import my ready-to-use Project.

Now you have to implement your new counter in Kustom. To do so simply add a Text item.

Press on "Text" to open details. In the details press on the text to open the edit screen.

Here you have to change the function to "$br(tasker,whatsapp)$" and confirm with the check mark.

Note: If Kustom doesn’t show anything at the beginning, the variable is not declared and not transfered to Kustom because there was no new notification yet. Simply go to your “NewWA” Task and press Play!

Now your Kustom Tasker setup is finished and you can customize your counter. Whatsapp was just an example, this Kustom Tasker guide works with every app that has notifications. Try it with Facebook Messenger and Google+.

Limitation: With this Kustom Tasker setup Tasker only knows that a notification is displayed, but not the content of it! For example, if 2 emails arrive at the same moment, just “1“ is added to the count!

If you want to do this with a lot of Apps it is easier to clone the Profiles and Tasks and adjust the settings. Don't forget to change the Variable everywhere!