Of course it's not "right" to put a Chebby in a Cobra, but even a Cobra with a Ford in it will still only be a replica, not the real thing. I'm from Germany and the market for Cobras here is small, but there is one. And it doesn't seem to make a difference in value if you have a Chevy or a Ford power plant in it. Most Cobras here have Chevy engines in them and parts for Chevy motors are much cheaper and more readily available than for Fords. I would probably go the Chevy way. But that's just an opinion from another Europe-based guy.
As to the engine itself, I can't give you all that much advice, because I'm not in the racing business. If you have 3 or 4k to spend, then I would still check out the price of different parts and get the good stuff for cheap money, then you can buy more good stuff. I'm not sure about the prices in the US, but here it would be cheaper to get for example a Scat rotating assy, costs a good deal less than the Eagle and is the same quality, as long as you stay under something around 600 HP. I would definetly go for the roller setup on cam shafts, they're expensive, but they allow for better flow, because the valves are open high for longer even on a shorter duration cam. As for the heads and exact figures ask the others guys on this forum, they can certainly give you better advice than me. Just wanted to say, 3 or 4k sounds a lot, but you'll see that it's spent much faster than you think if you're not careful.
Hope that helps you a bit,
Mad

PS: A Cobra is a very light vehicle, watch out for traction problems, they're more than likely to occur if your power is too high and the rearend not firmly on the ground. It's not only the weight-power ratio that gets you moving down the track...