Hmmm, I'm not sure which of the two I'd pick - Sonora to Donner or Tuolumne to Echo. You are choosing between northern Yosemite vs. the Desolation/Granite Chief Wildernesses. Both areas are very nice. Depends on what you want from your trip. That part of Yosemite offers incredible solitude. Desolation/Granite Chief have no solitude, but a thousand different lakes to enjoy, and of course great views of Tahoe.
The stretch from Tuolumne to Sonora Pass is a fairly long way without resupply. It's also a lot of up-and-down. If you do that section, save it for last. (So: hike north-to-south from Echo.) You'll be strong, can hike longer miles, and therefore carry a bit less food weight in the Sonora-Tuolumne stretch.
Desolation/Granite Chief Wildernesses in some ways are a better pick for newbie backpackers. There are bail-out points. With all the lakes and side trails, you can schedule your hike with some flexiblity - e.g. camp-to-camp today is 5 miles, but if we have extra energy that day we'll drop our packs at mile 5 anyway, and then go for a day-hike exploring one of the side trails/lakes. So, I suppose I'd go north-to-south if I were doing that option, just so I could start with the flexibility in the Desolation/Granite Chief areas.
For your overnighters: Kennedy Meadows is not a particularly pretty hike IMO. Start at Gianelli Cabin, also in Desolation Wilderness but a slightly shorter drive. Lots of charming lakes and meadows in there right off the bat. And, speaking as someone else who lives in East Bay, I do not find the campground at Chabot charming at all. Consider overnighting at Point Reyes, Butano State Park, Ventana Wilderness, or even Henry Coe.