Both kits were designed with the stock engine in mind, either choice that you make will work well with the stock engine. Any supporting parts that you have will only bolster the HP output. What are your goals with the car? Are you going to be mainly street driving or will you be racing some? Are you more focused on daily driving the car or showing the car? Do you have any modifications made to the car currently? The answers to these questions can help point you in a better direction.
We have installed blower kits on every kind of Mustang imaginable, some having very high mileage. One customer comes to mind that had 198,000 miles on his car when we installed the super charger system. Three plus years have elapsed since then and daily driving his car has added almost 40,000 more miles. The car has never had any issues as a result of the supercharger and continues to run great to this day. Just some food for thought.
Any questions at all that you might have about this, please feel free to ask!