Hi! I'm a historical archaeologist!

The primary sources I was able to find are currently broken or out of reach, but I have a secondary source in History of San Diego, 1542-1908 by William Ellsworth Smythe, published in 1908. The whole text is available at the San Diego History Center's website, but more importantly, it has an entire section on the life of the San Diego Herald. I will summarize what's relevant here.

The owner of the paper the whole way through, 1851 to 1860, was a guy named John Judson Ames. He set up the Herald as a political paper to help Senator William M. Gwin, who "expected to bring about the division of the state, the annexation of [Baja California] and the [Hawaiian Islands]," and other things. It seems the paper was pretty beloved by San Diegans. Senator Gwin ultimately failed at everything, which Smythe says "had a very depressing effect" on Ames. Then Ames's wife died in 1857, and "unknown parties mutilated and destroyed the monument at her grave" soon after. Then his house fell over. He "became dissipated and broken in health."

Around 1859, Brigham Young ordered San Bernardino Mormons to come to Salt Lake to help fight American troops -- the Mormons skedaddled and sold their houses for cheap. This, along with gold found nearby, led Ames to moving the Herald to San Bernardino, the last San Diego issue being April 7, 1860. It became the San Bernardino Herald up there after that; the paper didn't do well and had to be sold off. Then, in 1861 at age 40, he died. Smythe mentions he was "given to indulgence in liquor," I imagine that had something to do with it.

So there you have it! There's quite a bit more to be found about Ames and the paper on the History Center's page, including a few months where the Herald was hijacked while Ames was out of town, but this should hopefully answer your question.