340-360 vs 408-414

Everything is a give and take, and while there are empirical values that go with them, a lot of things people worry about are simply not that big a deal when compared to the benefits of a non factory stroke. Friction is important, but it's not a big loss an can be minimized further if you're really wanting to. Factory engineers were looking at warranty periods and emissions/economy, and these engines were designed in the 50s and tweaked in the 60s. Many of the truths they held in high regard have been replaced by newer thinking and technology.
So in regard to the OP - the 340 bores IMO are the only difference int he two choices (408/416) that will make any type of measurable difference between them. The larger bore is better for airflow and that can be measured. The main bearing size, additional piston material making the 4.07 piston heavier, additional friction due to more skirt/ring contact area, and the casting cores used when the blocks were cast all have very, very, very small affects on total output. Everything else is the same once you use the 4" stroke.