We're hijacking RenoFrank's topic. You guys should add a hike or two for him here.

John, to go up Cathedral Peak, I think it might be farther via the shortcut route, since you would need to circle back on the JMT to where that black line / divide appears on the map above.
Fish, I think they would require a Cathedral Lakes / JMT trail head permit, since you would hike to approximately the same camping spots. However, since trails connect from Tenaya Lake, the Tenaya Lake / Clouds Rest trailhead could probably qualify. But you might call their wilderness permit office and ask if they have any special "Cross country" permit quotas. Good idea on the starting point for your cross country adventure.