Nice choices first of all!

No question if it was me I would go with the 03 cobra.
First off you have a 4V, which means more room to grow.
Also, I believe the stage 3 has the smaller Eaton M90 as opposed to 03 with the M112 blower .
You have IRS on the cobra as well.

IMO the roush stage 3 is a GT with a smaller roots blower, body kit and improved handling.
You can change a pulley but basically its not too far from being maxed out.
Whereas many cobras have dynoed over 400HP to the wheels with an exhaust change and CAI.

Of course the roush has the distinction of a roush, limited availibility, looks, etc.

I guess it depends what you want out of it but I would go cobra every time.