I would go custom, Camshaft Innovations. The cost is more than worth it, when you don't need it anymore sell it. Your combo is pretty common for the most part and should not be hard off load it.
I installed Team Z Motorsports threw the floor connectors, its work but not bad. When I had questions Dave was more than happy to guide me along and provide pictures. There customer service is excellent. Give them a look:
http://www.teamzmotorsports.net/
The GT-40 is no longer manufactured because it was expensive to manufacture. If you see it in a Summit cataloge, get a new cataloge, yours is too old. If you want one, your going to have to get it used. It will cost you between $400-$600. I got mine off NMRA classifieds for $400(I went with...
If you don't have alot of cash to throw around, I would go this route: Keep the Cobra intake, get a custom cam, a good set of rockers, and go with Thumper of Orange Park heads. This would save you cash and out perform the combo you described, IMO.
Never had trouble with FRPP TB's, all the ones I have used were of high quality. But it has been several years since I have bought one, and if the new stuff is like the Cobra intakes that are now asiain sourced, I would stay away. There has been many complaints about newer Cobra intakes.