Having recently changed jobs to downtown SF (1 Market, to be precise) I have been using Chowhound to track down good lunch places within walking distance. I have found most of the places recommended to be quite accurately described, and there is MUCH better selection here than in Emeryville (former work haunt).
On Melanie's recommendation, I tried Mikaku today, which is not exactly downtown - it's at 323 Grant, across from Hotel Triton.
It was pretty much as described in the original post, but we had two different items, so I thought I'd update some other dishes.
First was a two-item bento, with tonkatsu and vegetable tempura as the two mains. I would give the tonkatsu a 7 or 8 (my ultimate 10.0 point reference tonkatsu is located at an 8-stool tonkatsu-ya in downtown Tokyo, near my old office. Incredible). Crust was decent but a bit thin, pork was thin and relatively moist & tender. Sauce seemed like standard Bulldog, not homemade, but not bad.
The veggie tempura was pretty poor. Not hot, kind of chewy batter, and mushy veggies. The reason I would cut them slack is we arrived shortly after 12:00 and it was VERY busy there - I think they pre-prepared them and had them sitting, waiting to be served.
The other lunch was the nigiri sushi special - 7 pieces with an additional 6-pieces of unagi roll. The unagi roll was good, but too much avocado for my taste. The sushi was decent, but some of the fish (hamachi, ebi) were a bit mushy - perhaps not defrosted? Tasted fresh but a bit soft for my taste.
The other items were fine, with the cellophane noodle salad as described by Melanie, good bowl of rice, good tea, and decent but unexceptional miso soup.
Overall, I'd give the place a B or B- rating, and would consider returning there to try the noodles, or given that it's nearly summer, the ten-zaru (tempura with zaru soba, a classic summer dish in Japan).
If anyone has other good Japanese suggestions, let's hear them!