[Jim0000]

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(If you select the correct receiver input during setup ... and you have if other channels work) Setup doesn't change whether you have yaw "receiver activity" or not, so that wiring configuration should still have yaw receiver activity after setup.

If the CC3D can save settings (you are running the fixed firmware that matches "Help -> About LibrePilot - Revision:", so it should) and the wizard yaw stick motions are done right, receiver activity on a channel should make setup connect that channel to yaw.   
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After reading your explanation above, I realise that at least part of the problem might be my level of confusion and beginners ignorance.
My total lack of understanding of these two sentences are an example of this.

Jim.

[TheOtherCliff]

General translation: 

Sorry, was trying to cover all the surrounding caveats in once sentence. 

You need to find a way of wiring receiver to CC3D that works for all 5 channels ("receiver activity"), and leave it that way forever.  It doesn't matter what is plugged in where since setup handles that all for you.

After getting the wiring right, you must run setup after that.  Setup says "Wiggle the yaw stick."  "Ahh, I see activity on channel 6 (or whatever # you used) so I will configure the CC3D to know to read the yaw value from channel 6 from now on.

If the wiring is correct, then the "receiver activity" box on the Input page works whether you wiggled the sticks correctly during setup or not.

If you have "receiver activity", then setup should see the activity channel number and assign it to the CC3D yaw function.

It really is pretty easy to just configure the yaw channel manually (Input page) by copying values from a working function like roll, and using the channel number that you see in "receiver activity."

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Now the caveats / additional information:
- The CC3D must be able to save settings.  Since you are having problems, it is a good idea to make sure that the CC3D Erase Settings bug isn't biting you.  Flash the fixed firmware that matches your GCS, and leave that firmware on it.
- If you flash the fixed firmware, you need to make sure that you use the correct firmware version, the version that matches your GCS version ("Revision:" as described before).
- You are using PWM inputs which is the default.  If you weren't, you would either need to run setup or do some small configuring before "receiver activity" would work.  As it is, power it up with default / erased settings and "receiver activity" works with no changes.
- All 5 "receiver activity" channel numbers must be different/unique, for instance it can't be seeing roll on #3 and yaw on #3 also.

[Jim0000]

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It really is pretty easy to just configure the yaw channel manually (Input page) by copying values from a working function like roll, and using the channel number that you see in "receiver activity".
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I don't understand this sentence Cliff.
Where are the values? And where are they changed or replaced"?

[TheOtherCliff]

Input page:  GCS -> Configuration -> Input

Flight battery plugged in, GCS running, USB plugged in, transmitter on, wiggle the sticks, do you see "Receiver Activity" (top right corner)?  There might be a second or two delay from stick motion to receiver activity.  Copy the Roll line values to the Yaw line.  Wiggle the transmitter Yaw stick to get the yaw channel number from "Receiver Activity" and use that for yaw "Number" column.  Press Save.  Reboot CC3D and test.