I can't tell what is wrong by the photos. The bottom leaves turn yellow when they need fertilizer. With all of that rain they might need to be refertilized.

Judging from the color of the new growth, the plants are taking up plenty of nitrogen and are poised to make vigorous growth when they get warm sun.

The older leaves are stressed and probably incubating early blight, so I would go ahead and clip them off. A leaf with more than 30 percent of its photosynthetic capacity offline is not worth keeping. I would also mulch with something to help keep the leaves dry -- plastic or cloth if it keeps raining, grass clippings or rotting wood chips when the rain stops. The mulch will also encourage more shallow roots to grow, which will serve the plants well in the long run.