Actually I think Jim Coogan plays a C#/D - the difference is important. (The outer row is the first of the pair.)
The advantage of having the main row on the outside is, I am told, that the outer row is generally slightly more powerful. The disadvantage would be finding a box in D/C#. I think you'd have to order a new one custom-built, or trust your luck in the search for a 2nd-hand box, which might take a long time.
C#/Ds are much more plentiful, as you probably know, even if they're not so plentiful as B/Cs, which, with all the arrogance of a total beginner, I consider a perverse system (* ducks to avoid missiles thrown by Chris Laughlin and TeriK *).
If it's a question of the sound, consider the Saltarelle Irish Bouëbe. According to info. at the www.buttonbox.com
, it has "innovative features: the inside row operates the upper row of pads for a bigger sound" - plus (incredibly useful) a stop on the bass side to remove the thirds from chords, thereby allowing you to play basses against minor melodies.
If it's a question of duplicating Cooley's playing style exactly, well that's another question. I thought he played a C#/D, but your question makes me think otherwise. Do you know for sure?
I can't really tell you about the differences in playing between the 2 systems. If you're playing on the outer row, I think that playing rolls might be a lot trickier. Mind you I also think that rolls usually sound pretty ghastly on the box - Cooley's being a notable exception.
At any event I think contacting Jim Coogan is a good idea. You might also post your question to the irishbox group on yahoo ( http://launch.groups.yahoo.com/group/irishbox/
) where there are people who know a lot more about the subject than me (I'm in the C#/D kindergarten at the moment).