What size are the primary tubes on the FMS shorty headers? 1-1/2" or 1-5/8"??
What size would JBA plan on running if they made a knock-off of the FMS headers?
I think everyone would much rather have an option of some aftermarket headers, rather than having to go custom (expensive) or go with the Ford factory units (expensive). Even if they are just a knock-off of the FMS headers, they would have to be better than the stock units. For JBA to go with a slightly larger tubing than the FMS units, it would not involve that much extra work.
However, JBA doesn't always suggest that bigger is better.
I know that on my 88 5.0 with the 1-5/8" shorties that I put on it, the primaries are still bigger than the actual exhaust ports. I realize that this may be on the older E7 heads and that they do not flow as well as the GT40's, but even still, I think anything over 1-1/2" or 1-5/8" primaries would be overkill. Even JBA recommends that for the 96+ DOHC cobras, one should stick to 1-1/2" shorties if you don't have aftermarket heads, porting, etc.
Just my .02 on the situation.