The GT40, Cobra and Explorer all share the same basic lower. All 3 have very similar flow numbers - allowing for the differences that always occur between flow benches/operators. The Cobra and the Explorer have a cast upper; the GT40 has a tubular upper. The GT40 upper weighs several pounds less than the other 2. The GT40, the early Explorer (95 through early 97) and the Cobra upper will allow you to basically bolt on your egr equipment. The later Explorer uppers have no egr provisions. On some of them (depending on year/application), you may have to relocate or drill/tap for the ACT sensor.
If you have to have functioning egr, stay away from the later model Explore uppers. Any of them are a fine upgrade from stock, and contrary to popular myth - all 3 are competitive with most of the other aftermarket intakes out there for mildly modded motors that are peaking under 5500 rpm. They may actually show better low end and mid range average torque than some of the short runner aftermarket intakes.
Forget about HP claims - what happens on your motor is gonna be a function of it's state of tune/mod. If you're running a stock intake - that lower is the most flow-restricted piece on the car.