Intake swap is not worth in my opinion. . I would do cam first then heads . . If I was going to do it in steps..
Nope, other way around. Cam will do nothing with the stock heads except move the power band, possibly lose power. There are actually a decent number of cars out there with the stock cam and aftermarket heads/intake and they'll make a solid 280-290 to the wheels in a HCI car while maintaining bone stock street manners/driveability.
To the OP, you most certainly will see a gain by doing the intake manifold but it won't be the drastic gain some may claim. I've done it, you can tell by the SOTP-o-meter that the car is faster but again, not drastic and not worth it with the stock heads IMO. Now... I would be very VERY wary of any ported intake manifold if you don't know exactly who did the portwork and have the receipts to back it up. Most people who get these GT40 intakes ported have Tom Moss (tmoss) do the lower and he is the #1 porter you want to be doing it. The GT40/Cobra/Explorer upper does not need to be ported btw, it already flows 250cfm. The lowers flow 200cfm in stock form and tmoss takes them out to 240-250 cfm.
As for the rest of the OP's proposed combo... I'd think twice about a few things.
1 - The E cam is not the best cam in the world for driveability or power. 110 LSA can cause some issues with the computer and even if you are getting one for $100 used, you can also get a TFS1 cam for $100 used and that is a much better cheap cam.
2 - GT40X heads are overpriced and underpowered. Unless you are getting them new for $700-$800, don't bother. Buying new I'd recommend the Trick Flow Twisted Wedge 170s.
3 - You'll spend the same or less money supercharging what you have vs doing a HCI, and be ahead 100+rwhp. Been there and done this, if I ever get another 5.0 pushrod car it will get a supercharger and I'll call it a day. If you are really feeling froggy you can pick up a set of GT40 irons from the JY and a GT40 intake. Have the heads cleaned/valve job/new seals/new springs and clean up the intake as well. You can do the GT40 irons and not spend more than $500 total, the intake you can get for $100-$150 all day if you look. Do not port anything and just bolt them on with ARP hardware and the stock GT cam. Then supercharge. That's a 425-450rwhp combination right there and will also get you bone stock street manners and 25mpg too. Even if you stick with the stock GT heads/intake you'll hit 400rwhp no problem.