Harris' claim is that "we value these things only in so far as we judge them to be part of the second set of factors conducive to (someone’s) well-being."

A virtue-ethicist may have a conception of the well-being of an agent according to which her moral integrity is more important than the overall consequences of her actions.

This is a strange definition of well-being and if we use this definition, Harris' claim that we can measure well-being with science and therefore discover moral truths is obviously false.

Harris wants to argue that well-being should be understood along lines that are measurable by science, but his (more general) claim that "we value these things only in so far as we judge them to be part of the second set of factors conducive to (someone’s) well-being" doesn't depend on that reading.

The point is only that an account of the good that is concerned with human well-being need not be consequentialist.

Well, we could define "wellbeing" as "always telling the truth, no matter what," but it would be a little weird of us.

"Somewhat arguing from the same place" isn't the issue. I'm somewhat arguing from the same place as plenty of people whom I would never endorse.

I AM LAZY. I love how, if I have even the vaguest recollection of having seen a website, I can easily find it again with 2 minutes of Google. But if I know the subject of a study, how it was conducted, and what the results were, it's still goddamned impossible to find. Hatehatehate the way research is published. Anyhow, I believe that this is a research "hot spot" now, even in the field of positive psychology which I loathe with all my power. Happiness research is very interesting and often not intuitive, and I recommend reading about it.

Here and here and here and here are some studies noting the effect. You can find a lot of vague references in Google by looking at terms relating to left prefrontal cortex, right prefrontal cortex, happiness, mood, depression, sadness, and so on. This book has references there, and this one. There are other studies but I can't find a good, solid online index/summary of the science. If you're interested in more you'll have to search around on your own.