The Ford Racing Cobra intake will work great with the stock heads. The Edelbrock Performer and TFS Street Heat would be two more good options.
As far as porting goes, yes there is more power to be had from porting the stock heads. But you really need to know what you're doing. There is more to it than just whacking out as much iron as possible. I recommend that whoever you have port them has some previous experience with the E7TE heads. As far as the valve springs go, there are millions of aftermarket parts for these cars so finding springs shouldn't not be hard at all. Check out Comp Cams or any other of the big valve-train companies and they should have several different options for upgrades.
As far as the suspension goes, there is a million different ways you could do it. Basically, I'd say some 70/30 struts (for a street car, 90/10 if it's mainly track only), drag shocks, some drag-oriented springs, and some lower control arms. This will get the basic parts of the suspension where they need to be. Once again, there are tons of manufacturer's that make these parts. However, I will recommend that you check out Maximum Motorsports :: The Leader In Mustang Performance Suspensions
. I belive they have an entire drag racing suspension package, and their parts are top-notch.