I don't think you will run into any extra bottom end issues due to the car being a stroker. Since you are running a supercharger this might be a good mod for you. FI cars benefit much more from the added stroker. As hotmustang said BB will get you more and BB/stroker is the best but for the price with your supercharger a stroker motor like that will work nice, but if you don't mind the extra cost I would consider a BB/stroker

i can't make up my mind...i already bought everything to build my Teksid with Manley forged stock replacements but i feel like i should sell my 4.6 manley pistons and send my block/cobra crank/manley rods to VT to be bored and sleeved while i have the chance. Oh the choices...