If you're planning to install rods, fit a large port head while the small port is off. If you're not fitting rods, the cost and effort of changing the heads isn't really worth it. Large port does allow more flow, but it's at the sacrifice of torque low down.
I really only fitted an AGU engine to mine because I got it stupidly cheap (£150 for the whole engine with everything still attached), and because it made the whole rebuild process 100% easier doing it out of the car.
If you're planning to go all out on the build, and you are trying to extract every last ounce of power from the engine, then yes, large port is worth it (the other advantage of large port engines is the "better" compression ratio, which you won't gain from if you just change the head), but otherwise, you would be better spending the £200+ it will cost to do the head swap on water/meth injection, and actually reap some real world benifits.