318: too much cylinder head?

What are the potential pitfalls of putting "too much" cylinder head on an engine?

There are many pitfalls. Please note - the engine in that article was a 4" stroke, had a thousand-dollar-plus set of rockers on it, had a one-off cam drive system, and no water pump on it. Going by what I've seen posted for dyno sheets they test them with cold water temps (under 150°). So my advice is take it all with a grain of salt because that is not something you'll have in a street car. Impressive, yes. But not easilly or economically repeatable in a street car.
In regard to your plans - the stroke is the key. A 3.31 stroke is easy to "over head". The RPMs in thier out of the box form are good, but are almost too big in terms of volume as-cast. IMO - it's a mistake to port them larger, and install huge intake valves to run on a 318 unless your peak power needs to be made at 7K rpm. You will hurt the flow potential in the area you will be running them in, and in turn hurt throttle response and torque right where you need it most.