Hi ssirlin,
I would have to recommend the stroker motor first. You will not gain enough HP or Torque by putting on the FI to notice. (Unless your current engine is under-carbureted with a bad intake as well)
You could possibly improve the driveability with the Hilborn unit after much sorting.
As to size of the engine, this will have to be determined by what you wish the power curve to be like.
I recommend that you go to:
Butcher Desktop dyno fantasies
You will find more info there than you need to make a stroker choice.
Of course, he is the "Butcher" so be afraid, very afraid, that mysterious things will begin to happen to your Cobra once you start down the Butcher path.
The only known cure once you are on the Butcher path is a McMaster-Carr catalog and a complete inventory of Loctite products in the industrial size.