The real answer to your question, I think, is what does your power band look like? The whole point of gears is to adapt the car to the available power band, such that you make the most out of it. I apologize in advance if this obvious to everyone. Depending on where your power band starts and tops out, you could run, for example, 2.37's and that would be perfectly fine (read: fast). I'm not suggesting you do this, I am merely trying to point out that the gear selection has a lot of variables. Do you drag race? Do you care about top end speed? Without going into the reasons (I will be happy to if you would like), I would think 3.55's would be good - you have tons of power. Granted I am not super familiar with the 96 Cobra's, so there's my disclaimer. But at your original WHP, you were putting about 5000 WTQ (give or take) to the ground in 1st gear. Granted, not for very long, but I'm not sure how you didn't boil your tires (unless the Cobra is really heavy or something?). Even with 3.55's, you will be putting about 4300 WTQ down (give or take). That's still quite a lot. If you have a problem with tire slip from a start, go with higher gears. If you are gripping like a sumabeech with no tire slip, keep your current lower gears. Personally, I think 4.1 (and maybe even 3.73) is too much gear, but again I have no experience with this car. And also the rest of the internet says stuff like "4.1, 4.56, don't fear the gear, blah blah." I don't know. In the end, you are making the same power either way. Your car will be fast either way. Drag racers use gear to minimize shifts before the 1/4 mile marker. You drive your car in the real world. I would think having to shift all the time would be annoying. (Unless you drag race it?)
Another way to think about it: 4.1's mean you won't hit 60 mph in 2nd gear, it will require you shifting to 3rd. 3.73's will let you get to 60 (and just a bit past) in 2nd gear. Which do think is faster? The car that has the extra shift, or the one that doesn't? (Hint: usually it's the one that doesn't. Ask me how I know.)
Remember, the Torque you get from lower gears isn't free - it means the engine has to spin more. Which means you don't get as many revolutions of the tire in that particular gear. Which means you don't go quite as far (which is also why your mph is lower). Now, you have more Torque to help you go, but you still move through the rpm's very fast. If your car has a nice flat power band that's decently wide, then you would be better off with lower gears to take advantage of the average power your engine produces. If your car is peaky and has a very narrow power band, especially up top, then you are better off with higher gears to help you get there quicker. Also, the butt dyno will tell you that lower gear is faster because you feel the g's more. But keep in mind your butt dyno can be deceived. Just because a car feels faster doesn't mean it actually is.
Lastly, a good analogy is this: lower gears (4.1) are like sprinters. Quick of the line, but die very soon. Higher gears (3.27) are like endurance runners. Not the fastest in a sprint but will go a lot longer. "Middle of the road" gears (3.55) are just that. They are a compromise. One could argue they are good at neither, or one could argue that they exhibit some of the better qualities of the two without the extreme downsides. Ultimately, it's up to you and how you want your car to drive. If you felt 4.1 was too much, try 3.55. If that's not enough, then it looks like 3.73's are the ticket
Edit: I forgot to add: if your goal is to get the fastest possible car and don't care about redline or top end speed, go with the lowest gear you can stand (and that will grip).
