I have a 2 dr manual with 3.73 on order. Hopefully will come in this week or early next. I'll let you know then, hehe.
I had 3.73 on my 08 jku with manual shift and it rode just fine. My wife has 3.21 in her 2 dr 2012jk manual and it rides just fine.
If you are in doubt I'd say go with the 3.73 gears.