I would keep that EFI Spyder intake on the 408 for sure. That isn't the top intake but it is close, and the GT40 is way far away down the list.
Your heads aren't the greatest either but given the 408 CI and a good intake, a custom cam would more than hold it's own against any similar weight vehicle.
You didn't mention many details about that engine before, and I figured you would see the light and stay with the 347. Since you are going to make the Windsor work, I would rework the heads to match a custom cam designed just for that truck and engine. That cost would be minimal, if the engine was out. I know how much trouble it is to R&R that engine, it's a shame it couldn't have been done before.
FYI, a proper custom cam will be designed to include use of valve springs which are not used in OTS heads or typical head builds. Meaning when planned for, a custom cam will be designed to utilize specific springs(likely stiffer and with tighter coil bind) that 99% of the time are not on existing heads. So done right a custom cam is made, and the heads it's made for are then set up with different springs(specified by the cam designer). It all adds up to more rpm acceleration(not dyno power), plus the best driveability.
A custom cam made for actual specific heads and intake will not be down on power at any rpm(any rpm), compared to any smaller intake, heads, or OTS cams. That does not apply to parts which you or I select, it only applies to parts and cam designed by a cam expert. BTW, the big cam companies do not qualify as cam experts. Their tech line guys are paid to sell you one of their OTS cams. If you insist on paying them extra for a "custom" cam, they will throw one together, but it's nothing like the real deal from the real cam guru's. The best I know of for Ford cams is Jay Allen, who is not available right now. The other I hear of a lot is Ed Curtis, but I don't know enough to really endorse him. He likes AFR heads, and that to me is a black mark, those are not the best Ford heads at all.