gt40 and cobra and pretty much the same thing, professional products intake is an edlebrock intake knock off, with cheap castings, maybe perform better? someone chime in on this here.
The Typhoon is supposed to be just as good as the Edelbrock version as long as you clean up the internal casting. SO if you have a grinder and sanding cartridges I'd go that route. I've been kind of leaning toward one of those myself once I decide to move away from the GT40.
I have run a combo in preaty much all the configs. you are asking...
When I first put on my gt40 heads (un-ported) I had Tmoss port my factory lower. The ports on the ported stock lower after porting and whathaveyou was about as dead on as possible without actually getting the heads to the porter to match up. They were about perfect. The work on the rest of the runners was also VERY good. With the un-ported heads, TFS1 cam, and that ported stocker untuned I ran a 13.5 @ 102mph not bad. It ran great for the parts on it.
I got the gt40's ported (BIG thank to Thumper) and also picked up an exploder intake. Tmoss (also BIG thanks) ported that lower for me to help it better match the now better flowing gt40 heads. I just got it back up and running a few weeks ago and it was actually the last day of the year for the track to be open so I dont have any times. I took it out a few weeks ago and on the hwy out ran a ws6 ls1 though and it felt great power wise. A local dyno shop is having a "winter dyno league" that puts you threw a 1/4 mile run and for 20$ I may go next fri and see whats up.
You'll lose a bit of bottom-end torque in favor of top-end power with the PP, and you'll essentially get roughly the same performance out of the GT40 and the Cobra. Personally, I'd go with the Cobra. I've heard too many bad stories about the fitment and quality of the PP, and Cobra's are easier to come by and cheaper than the GT40 (I'm assuming you are reffering to the tubular version, which is no longer produced). Or, better yet, get an explorer intake for even cheaper.
i just picked up an explorer intake for 70 bucks, and its the same thing as ford sold as the gt-40 for hundreds more. theyre really easy to find too, i got mine at the first salvage yard i went to.