Indeed the Ektar (and presumably Portra 400) is tough to optically focus. I use the Peak Model 1 (the big one) and it works pretty well, but having an edge or some contrast in the neg really helps a lot. Focusing on a featureless area of the neg is next to impossible without several tries. (The Beseler 45A head doesn't help either, with the pseudo-continuous light via high frequency flash tubes....)
But yes the results (at least on the Ektar) are superb! Looking forward to trying the portra soon too.