I think the OP's question regarded a 408 variation of a Windsor versus a 427 variation. Assuming that is the question, here are my thoughts.
- The main difference between a 408 small block and a 427 small block is that the engine displacement will match the badge on the side of the car. That means you can answer the inevitable "Does that have a 427?" question with a simple yes. Of course the questioner was likely thinking of the legendary 427 side oiler, but he'll be happy thinking he just saw a car with one.
- All other things being equal, the 427 will produce a little more torque and HP than the 408.
- The connecting rod geometry get more extreme as the size of the stroker crank (and displacement) gets larger. That places more side stresses on engine components and might result in shortened engine life. That is the argument presented to me that led me to opt for a 408 size crank rather than the 427 size.
- Given how little many Cobra replicas are driven, I wouldn't be too worried about the larger crank.