In order for everything to be fake it would require a level of understanding, resources and cash up front well beyond the return. All in the hopes that the games would sell?
Assuming that these AF3's simply contain the boards of legit SW3's, then all you would need is 6x complete SW3's and access to AF3 MVS (artwork) & AF3 CD to create what is required, utilising industry standard design software (Ps, Ai etc), a decent scanner and access to digital print. Now, the work involved vs the payoff ($100k) is worth much more than the amount of time and money injected to bring this 'project' forward. And, to be honest, you didn't have to do this all by yourself. All you ever needed was someone else who know what they were doing. For example, someone like me.
I've been working in print and design for over a decade - day in, day out. I work for a big international company who happen to have all that necessary equipment onsite - Macs, Software, Scanners, and big iGen4 printers used for daily print runs - ideal for a short print run all for the cost of stock and a 'click'. It's who you know and all that, and I hate to say it, but if I were so inclined, I would be in an ideal environment to undertake such a task for a fee (nothing spectacular, just a designers fee).
In the right situation, it would be VERY worthwhile you, or anyone undertaking such a project to bring about $100, I'm afraid to say.
I didn't know anything more than you did about the insert until it was pointed out in the past few days. Did SNK ever cut corners when making inserts and manuals? All the time. But no one is interested in that. I don't have every game ever made but just picking up the manual for the Japanese far east of eden (KK), page 14. The entire manual looks poor but at least it's consistant, then page 14 takes a dive. Why? Because it's a scan and a poor one at that.
Hmmm. I didn't mention this until now, but I had a look back at the first page of scans this afternoon just for perusals sake and I did notice something in the scans that falls somewhat inline with what you're trying to imply:
Now, more obviously, in the 4th image along, you'll notice a terrible amount of "moiree" present in the girls skirt. However, if you pay close attention to her shirt/blouse in the previous 3 SNK printed scans, you'll notice the same pattern is present in those too - a pattern which is only ever present as a result of scanned print. Basically, I'm suggesting that SNK used a scan of some description for this manual and then it was re-scanned for the AF3 US manual resulting in the additional moiree present in the skirt. I believe it would be present in the blouse too, however, the contrast & brightness of the scan here unintentionally eliminates the original moiree...