Nix Mills

Ouch. I wonder if there's been an update to the weapons effect. We'll check and update. Thanks for reporting it.

That is unfortunately a Core DCS bug. If it persists,
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Thanks for reporting this. I was a bit surprised to see this as the Guard frequency was not actually controlled by the missions but a native DCS setting.
It would seem that one of the recent DTC updates might have broken the Guard setting. For now, I suggest you simply put 243.000 into channel M (manual).

I think the default gun settings are fine, as long as you're in A/G mode and CCIP mode.
Try to also make sure to have my radar altimeter on (ALT switch down to RDR), set your minimum altitude (e.g. to 500ft) and then select the HUD with Sensor Control Switch 'up' - the switch on your stick that you also use for selecting left, right and bottom DDIs. From what I understand, this enables your gun sight to accurately calculate distance to target and elevation, and all you need to do is point straight at the target and fire.
Do however make sure to come in on a ~30 degree angle - too low makes it difficult to hit the target, too high makes it difficult to pull up in time.
Let me know how you go.

The channel switching is a bit tricky there because you had to monitor Israeli and Jordanian airspace controllers also.
If you switch AUX back to channel 1 (305AM), you can order wingman to tanker. To communicate with tanker (request rejoin), call Shell on channel 19 on PRI. When you're done refueling, switch back to channel 7 on PRI so that you can monitor Image and keep AUX on channel 1 so that you can communicate with wingman.

Thanks for reporting this. Had a similar report on Discord. For the update that just came out today, I see that I made a mistake in updating M14 in an attempt to delay start up, taxi and departure of 307 and 309 a bit.
Do this (just go with it): 
When you taxi out to the catapults and facing down the carrier deck (heading between 210 and 220, or so). Pull the hand brake, then release it again. 307 and 309 should now have pilots and be starting up. 

Thank you so much for that, IceyJones.
I have corrected the orbit reminder popup to say that you should be on 275.500 on COMM1. I have increased the trigger zone over Deir ez Zuir to a radius a little over 9 nm (it was 7 nm) and I removed a single insurgent in the town that could cause the AI wingman to return to attack that instead. We'll do our best to get this included next time they run a patch update.
I'm impressed that you're up to M12 already.

Thanks for the comments, @IceyJones.
The issue you've encountered here unfortunately is a DCS bug and it can be a little bit luck-of-the-draw whether or not it happens. It usually does not, but apparently here it's happening to you three times in a row, which is concerning. It sounds like you were doing all the right things, though.
If it continues to ruin your gameplay, read this spoiler.