What I did:

1. Tried to follow hints on transmitters. Shift-clicking (right, left) does nothing.
2. Removed two transmitters, not sure if paired - could not craft a pair again.
3. During rebuild removed all transmitters (8 pairs) - got 16 transmitters, could not re-use - each was claiming that other one does not exist (were looking for old coordinates), had to delete all of them and craft new pairs
4. Cannot see which two are a pair once placed in a world, no way to trace signal.

What happened:

I got frustrated and used different wireless transmission method (another mod, rftools)

What should have happened:

Once collected transmitters should pair and stack automatically.
There should be a way to identify transmitters when placed on wires and they should work without tying to fixed [x,z,y] - maybe convert to channels? Would make stacking much simplier as well, and maybe would allow for multiple receivers of wireless signal.

Used Versions:

• Minecraft-1.12.2
• AutomatedRedstone-6.1.4
• CD4017BE_lib-6.2.7
• Forge-14.23.5.2772

Sneak right-clicking on the block of a transmitter (that has a link that's also currently placed as block somewhere) with empty hand should remove both linked transmitters and give you back a "pair".
Maybe you already broke the link before attempting this or your hand was not empty or you had some item in offhand that consumed the right-click event.

Two transmitters should stay linked as long as, at any point in time, at least one of them stays as placed block somewhere in a world (any dimension, works even in currently unloaded chunks).
However as soon as you have both blocks broken, the link gets always lost (unless they are placed back to exactly where they were). But this is not an issue as you should be able to just craft any two single transmitters (not necessarily a linked pair) back together into a "pair" one.
Maybe you failed to do so because you didn't arrange the items horizontally next to each other in the crafting grid (the recipe is shaped). If this is really a confusion issue, I should probably change the recipe to shapeless.

Your proposed channel idea with multiple transmitters in one channel unfortunately would require me to rewrite my entire multi-block network system in order to support nodes with a non fixed amount of vertices connected to it. And for me the benefits are too small to be worth it.
Currently these wireless transmitters work by just tricking the attached cables into believing they were placed next to each other by simply forwarding their capabilities.

Hm. I think I tried sneak-clicking with empty hand as well. Might be that I was trying to get pair that was no longer a pair because I messed which one is paired to which one...

The transmitters indeed stay linked as long as I move only one of them at a time.
But it is still not possible to check which one is paired to one that you are holding...
Integrated Dynamics have omni wireless transmitters - they are crafted in pairs and each pair forms a group (of two). Right-clicking on omni-connector gives you a message with channel number. Each pair gets next group number. A single number is a lot easier for human to process then [x,z,y] when checking the cabling. I mean, it works, but I have to usually physically go to coordinates from tooltip to see paired connector... and when there are many near it gets confusing sometimes.

I guess changing recipe to shapeless would clear some issues. I think I tried 2 horizontally, but probably from middle slot... not that it should matter? Will try again, maybe I just missed this one good layout by accident.

Multiple transmitters idea: no problems, it is easy to work around it. I had no idea how it was implemented.