I would agree with the others that exhaust is a very big issue, but would add the following:
Cooling - minimum 3-row radiator with better fan and shroud should be used. Make sure that ALL cooling components are in top shape.
Differential/Driveshaft - If your engine will put out 350lbs of torque, particularly for manual trans cars, you should think about upgrading to a 9-inch. That requires a modified driveshaft, too.
Suspension/brakes - Ws weigh about 75-100lbs more than a 289 if you are not going with aluminum heads/intake. This should require heavier (I used 620s) front springs and a larger sway bar (I used a 1-inch). Disc brakes are a must on a car with more power and more weight in the front end, too.
Engine mounts - Make sure you are using the late 66 mounts with new insulators. Otherwise, your headers will hit the shock towers most likely.
IMO, the swap is not exactly the "piece of cake" that some suggest, but it is well worth the trouble and expense if you are a torque addict.