That's an interesting top end power curve, it might be something like the cats. The GT40 parts should have no problem supporting 5000rpm and more for the 302. There haven't been a lot of dyno test done on Explorer engines with the truck roller cam. I think that cam is good enough to not fall flat before 5000, but there aren't many dyno charts you could compare with. My three 302's have all shifted stock at 5000rpm, but that's bone stock with no pressure from a supercharger.
Your valve springs may also be a possibility also for hurting the top end there, it may be some valve float. I'd ask your shop if they think it's more likely the cats are partially clogged, or the old valve springs. I tend to think the VS are weak, and you might find out by building a bigger cat pipe as a next step.
That Vortech intake is an old model that is better than the GT40, it's similar to a model of TFS intake. But I can't remember which one(rpm range), I had an old friend with one on his 93 Cobra convertible. For your future engine, it may be a good choice, the GT40 definitely isn't assuming you go bigger to say 347. Price might be a thought, the TFS R intake is a top rpm choice, similar to the Holley Systemax II, and the Edelbrock Victor EFI.
If you are becoming settled on that intercooler layout with the full upper/lower intake behind it, then I think one of those four might be th best end choice. So consider what engine you might end with, and pick the intake based on both looks and the rpm range it's made for. The three I mentioned I think can be had for about $400 or more, used, prices have been moving up. That Vortech I'm not sure of, that could be a rare and niche, expensive model. I'd hunt on the Corral to see what it is rpm range wise, compared to the others. If you could rebuild the intercooler system by placing one over the lower alone, that could save the cost of buying any upper. I got my TFS R lower and a Victor EFI, for about $150 each, several years ago. I didn't like the Victor lower, being so tall(tall lower runners, and short upper runners). The TFS and Holley have the shortest lower intake runners, with uppers that are a little longer.
