the sky is the limit with these cars and it all depends on what your goals are.
If your looking for a bit more grunt i would port the blower add a boost a pump, and Port the TB and plenum. My ported eaton with a 2.76 made 494whp and 486wtq (with a stock TB). If you go that route you will need to start thinking about a new clutch down the road. If you want anymore than 500-540 (blower only) you will need a twin screw or Nitrous.
Also, Long tubes for your mods are a waste of money. They barely add any power and are a nightmare to install. 03/04 cobras don't really need them until closer to 600 or more horsepower when they start being restrictive.
+1 on beefing up the IRS. an IRS brace, and some bushings will help. Halfshafts are a crap shoot. Some cobras are running around with 600hp on the stock halfshafts no problem, Some break nearly stock. It really depends on how hard you launch, which tires you run and technique. My buddy has a 99 cobra that was running around 500hp with the weaker 28 spline halfshaft. He is now closer the 600hp and just broke his first one. | 
