Code P0620, alternator fuse (#9) missing, fuse box location will not hold fuse?

Apparently, Ford changed over to their Smart Charge system in the 2004 model year with the Expedition. Mine was made July 2003, lists as a 2003, but I'm wondering if it might have the 2004 charging system? If so, I might have the wrong alternator even though it's supposedly the correct one for a 2003 Expedition. Looking at photos of allegedly compatible remanufactured fuse panels, some show a fuse in the #9 slot and some don't. Part number is 3L7T-14A067-AC. The user manual that came with the car shows a 10A fuse in that slot. Am I just wasting time trying to get a fuse in there? Photo of fuse panel attached. I pulled the fuse above it for comparison.

Yep, I think you have the 2004 system which doesn't have a # 9 fuse. I would check the alternator plug terminals and look for signs of overheating, if so, you need to get a new pigtail and wire it in. Also check the condition of the fusible links, here are both the 2003 and 2004 wiring diagrams for the alternator and charging system. Also, what brand alternator are you using? Check out the diagrams (below). Please let us know what you find. We are interested to see what it is.

I am pretty sure at this point that the alternator is defective. It seems to be the correct type, but never sends an amp output square wave (duty cycle) back to the PCM. See image below:
I don't know why your software rotated it. Hopefully you can copy and rotate it vertically as intended.

Alternator is Ultima R112019B from O'Reilly's.

The image is sideways because the image was taken on the phone in portrait instead of landscape, we are trying to fix it. Anyway, I would get an alternator from rockauto.com (Motorcraft) I have had good luck with the Motorcraft brand. This should fix your problem.

The mystery deepens. Returned the alternator for a replacement (same type). First rebuilt alternator produced similar measurements except GENCOM frequency was 170 Hz, GENMON voltage 8.8 V.

Here are my detailed measurements with the 2nd alternator:

A. 3-pin connector detached from alternator, measured at PCM
Key off, ohms to GND at PCM: GENCOM = 2.1k GENMON = 134k
Key on, engine off: GENCOM = 8.7 V DC GENMON = 0.0 V DC BAT = 12.16 V
Key on, engine on, idle: GENCOM = 8.6 V DC GENMON = 11.6 V DC BAT = 11.82 V
After engine rev to 2500 RPM: BAT = 14.29 V

B. 3-pin connector attached to alternator, measured at PCM
Key on, engine off: GENCOM = 8.7 V DC GENMON = 0.0 V DC BAT = 12.17 V
Key on, engine on, idle: GENCOM = square wave, ~9 V Pk to Pk, 133 HZ, ~60% +cycle
GENMON = 10.4 V DC BAT = 14.19 V
Turn A/C on: GENCOM DC = 5.8 V GENMON = 10.3 V DC BAT = 14.12 V
Turn headlights on: GENCOM DC = 4.9 V GENMON = 10.2 V DC BAT = 13.97 V

Here is what makes no sense to me:
Why does GENMON show a DC voltage instead of a square wave, and only when the engine is running? I thought this voltage was supplied by the PCM, to be manipulated by the alternator.

Why did the GENCOM square wave show a radically different frequency from the 1st alternator to the 2nd allegedly identical alternator? I thought this was controlled by the PCM, but it looks as if it is being set by the alternator.

Why does GENCOM show an 8.7 V DC level with the engine off and the alternator disconnected? I thought the GENCOM voltage was supplied by the alternator, then manipulated by the PCM.

With the alternator disconnected, key on, engine off, I would expect to see a source voltage at GENMON, and no voltage at GENCOM. Instead I see the opposite.

Even so the system seems to be charging the battery OK, and I have not (yet) seen the battery warning light come on since installing the 2nd alternator.

I am wondering if I might have a Group 2 system as described in this article?
https://www.electricalrebuilders.org/techlib/tech_articles/ford_6g_regulators.pdf

It sounds like the first alternator had a bad diode set and this one is better but not as good as it could be. Check the wiring diagrams so you can see how the system works. I would test for power and grounds and if okay get a third Motorcraft alternator. You should not be seeing any waves; the alternator converts the waves to direct current DC internally. There is a chance the PCM is going out which I have seen before after bad alternators have been installed. With the engine running can you see AC voltage at the battery?

By finding a site that sells alternator parts (https://store.alternatorparts.com/part-f603.aspx) and matching the regulator type to the original alternator OEM part # (2L7Z10346BA) I have determined that my alternator is a Group 2 non-PCM controlled 6G alternator, so the communication signals described in Ford Smart Charge system videos do not apply. Sorry for all the confusion. It seems to work fine, but I haven't found a good clear description of the theory of operation yet.

That is a good sign, are there any AC voltage reading at the battery when the engine is running? Does the system seem to be okay now or?