Thank you! I spoke with the dealership this morning and told them the software update does not take place of the cam phaser replacement and it is still covered to replace it. They let me know I'll have to pay for it to go through diagnostics and "then IF that's even what is the problem" it's on back order and can't tell me when it'll be available.
First off, there is no IF.
I am all too familiar with that sound. One (or more—there are four of them) of your VCT gears (commonly called “cam phasers”) has a broken pin. Point blank. End of discussion. It’s an internal pin that is supposed to briefly lock the two halves of the VCT gear together during cold starts until oil pressure is built up sufficiently.
When the pin breaks, the two halves of the VCT slap back and forth, creating that knocking sound, for a couple seconds, until oil pressure in the top of the engine builds up to normal pressure.
Secondly, the ONLY way to fix this is for them to replace the broken part. In other words they have to pull the front cover off the engine and replace your cam gears. This is what folks commonly call the “cam phaser replacement” job.
The PCM re-programming “fix” is just a bandaid that Ford attempted to prevent having to do more costly cam phaser replacements. It may help PREVENT or MINIMIZE abnormal wear on those pins inside the VCT gears. But once the engine sounds like yours, the damage is done. The pin is broken and the only way to make that noise go away is to replace the VCT gear.
Do not let them talk you off of this!
Once they realize you are armed with enough knowledge to call BS, they will capitulate.
And after they have performed the cam phaser job, my recommendation unfortunately is to sell it. There is a strong possibility that the oil flow problem at the top/front of your engine is going to cause the same problem in another 20,000 -30,000 miles. Even with their PCM reprogramming bandaid.