I did the JMT last year, and it was my first >6 day hike.
So first, some general notes I had from a first-longer hike:
1. Calorie requirements went up after day 5 or so. I usually plan for 3500 calories per day, and it's always too much. But on the second half of the JMT, I think 3500-4000 would have been good. I think PCT'ers plan on 4000 per day. If I were doing it again, I'd plan on 3000 per day for the first half and 4000 for the second half.
…okay, I guess I only had one general note.
More specific:
It seems to me–if you're not resupplying past MTR (i.e., you're not hiking out to Onion Valley, or having a resupply brought in by packers), then MTR is a pretty darn good choice–minimize the (already obscene) amount of food you have to carry on the second half.
How fast are you planning on going? That also affects the TM, Red's Meadow, VVR and MTR resupply choice. Last year, we went through TM on day 2 (didn't resupply, but stuffed our faces at the grill), Red's on day 4 (resupplied and stuffed our faces), and MTR on day 6 (resupplied only, because it's complicated to eat at MTR). VVR would've been on day 5. Since the lake was empty, we'd hike those extra miles for hot food, but we'd just had hot food the day before, at Red's, and we'd be at Whitney Portal in under a week. Going six days without a cheeseburger is not such a hard thing in life.
I hear that VVR is fun, though. Real through-hikey–part of the JMT culture; not to be missed. I want to go explore the Mono Recesses one of these years. Hopefully I will, and hopefully I'll swing by VVR for a resupply–and yes, a cold beer–when I do.
My only other advice is regarding your diet–I think I'm echoing the sentiments of posters above when I say three Clif Bars a day will be three too many after around day 4. My backpacking diet consists mostly of Pringles, Perpetuem, jerky and chocolate. A Hammer Gel and a Payday for breakfast. Cheese where possible, but I'm from Wisconsin–that's just kind of a credo.
I think the Mountain House meals pack terribly, and all taste the same. But, you've backpacked multi-day trips before, so you'll have tried to cram them in a bear can, and you'll have eaten them day after day. You know what you're getting yourself (and your cathole trowel) into.
Oh, and Starbucks Via is not bad. I'm a coffee snob (and addict), but I drink Via when I'm on the trail. It's not terrible, and oh-so easy. In my quest to go UL, I've stopped carrying a mug–I just dump a little of the Via packet into my mouth, pour some water into my mouth, shake my head vigorously, and swallow. Clears out the cobwebs, and there's nothing to clean. This should probably go in the Multi-Use Gear forum, now that I think about it.