Well, you asked for opinions and you definitely are getting that here. There are a variety of experiences and none are wrong.
The 427 Cobra transmission that I had was a big input, small output, 24", close ratio.
I do not think that there was ever a wide ratio box ever made by Ford for that application?
If you look down the list that David Key has posted, any original displacement larger then the 390 that he knows of is a big input, close ratio box.
The 390 applications are small inputs, like the 289's.
There are wide ratio 390 transmissions but are small inputs.
With Ford, it seems there is always a rare combination they made that was never made in mass quantities but did exist somewhere, somehow mostly unknown to even experienced Ford appliers?
I do believe though that in the original CSX 3000 cars, the most common, if not all applications was a 3.31 rear with a close ratio (2.32 first gear), 24" long, 1-3/8" big input and small (28 spline) output. So in my OPINION, that would be an original 427COBRA application.
One of the considerations on close v. wide ratio that is not mentioned here, is the smoothness the close ratio gives as you accelerate through the gears v. the wide ratio. You need to consider the wear and tear on the drive line because of the torque loading of the larger displacements.
The 427 Cobra is very sensitive to throttle input but more specifically, to torque inputs. You want to be as smooth as you can when driving it spiritedly.
You shouldn't compare another vehicle such as a big block "Mustang" to the Cobra application. They are not the same. They are beyond apples and oranges.
Many Cobra "kit" cars are not using IRS Cobra rear suspensions but solid axle "Mustang" variants. That changes the equation somewhat as well.
Initially, the 427 Cobra was subject to what was described as "snap steer". What was happening was that the balance of front to rear steering was not right initially.
I'm not sure of the EXACT formula that came to be for stabilizing the car but there was work involved which included a smooth transition of power to the car, which does include the transmission and rear gearing.
When you build your own Cobra, you are varying from the Shelby factories solution. You need to be aware that this is at your own risk and you are applying your own solutions which may need some testing to verify the car is stable even under normal driving not to mention track characteristics.
All vehicles with weight bias front to rear with the majority of that weight is on the rear, 40% front, 60% rear, are extremely susceptible to the rear suddenly steering the car. That IS involved in the "snap steer" issue.
One thing that you must insure is that the rear tires have noticeable toe in. Somewhere in the 3/16" to 1/4" vicinity. With an IRS rear that is adjustable. With a solid rear, it is not.
Someone asked here before, what are the factory suspension settings for a "Comp/SC Cobra". All they could find were stock 427 street settings. The reason for that is that each car needs to be set up individually according to it's track reactions. So therefore there is no specific setting, you just start with a street setting and work from there.
Why do I mention that here? Gearing of the car is involved in that. When you step off of the throttle, you don't want excessive rear end steer because of the braking effect of taller gears.
Honestly though, the only way that YOU are going to be able to determine the best setting is for YOU to experiment with these combinations.
Picking the gearing profile you like is probably close to trying to pick a camshaft profile that YOU will like rather then what was recommended to you by others. Simply put, each is going to have their own interpretation of what is streetable, what idles well and what pulls the best, not what others tell you.
Gearing is very similar. That's why people like Miles were at the "tracks" so often testing combinations. I'd go with his picks they put originally in the Cobras.
Again, this is my opinion. Others certainly have taken different avenues and likely may disagree.