The Dana 44's are very nice units and have served well for several decades, increasing power levels not withstanding. There is a relatively good supply of aftermarket parts available for them and by and large I have not heard of people who had any significant design, fabrication or installation issues with them. If I were going to use one I would definitely use one of the Kirkham units, that are easily the very best and nicest Dana 44's available anywhere today.
The other very good choice as several have already said is the 8.8 inch Ford IRS center section as used in several of their passenger cars. I would recommend you look for an 8.8 IRS housing out of an Explorer rather than a passenger car. The Explorer 8.8 IRS housings are by far the most robust of all the aluminum 8.8 IRS housings Ford has ever produced. Be sure you get a 2007 through 2010 housing. Those are the ones with the massive front ears for locating the nose of the housing.
When ACE23 was struggling with the same decision alternatives you currently are I posted up some pics and suggestions for him on the site here. This is a link to the post =>
Ford 8.8 IRS Suggestions.
You might find something in there that could be helpful as you go about noodling out the best alternatives for your build.
BTW congrats on the decision to do a scratch build. It is the best way to get your Cobra exactly they way you always wanted and thought they should be — lots of work but also lots of satisfaction and immense pride in the finished product that is YOUR Cobra.
Ed