Usually if plants have been subjected to torrential rainfall and have been standing in water, one problem that occurs is that the waterlogged roots are so clogged with water that they cannot take up nutrients from the soil. The lack of nutrients cause all sorts of issues from stalled growth to discolored foliage. When this is the problem, you don't need to add anything to the soil because the roots are too clogged with water to benefit from anything you'd add to the soil. Since you added so much to the soil this year, I wouldn't add anything else.

When we had an incredibly wet year in 2007, my plants stayed wet (even in raised beds) for a couple of months and mostly I just had to be patient and wait for the soil to dry. Once the soil started drying out a little, the plants looked marginally better. I then fed them carefully with Miracle Grow trying to get some nutrients to the plants without adding so much extra water that the waterlogging worsened again. I got a great crop of tomatoes that year, though they were later than usual. If I remember correctly, we had roughly a foot of rain in June following what had been a wet May as well. The soil didn't really dry up until sometime in July.

As for the issues on the foliage, without being able to see them, we could only guess what might me going on, but I'd suspect it was some sort of fungal disease. However, with all the rain you've had it could be bacterial. Or, it could be viral. Diseases thrive on tomato foliage in wet weather, especially if you're not using a fungicide to prevent the fungal diseases from attaching to the foliage.

I'm going to link the TAMU tomato problem solver. Maybe you can compare the photos there to what you're seeing on your leaves and can diagnose what you're seeing.

Dawn

Here is a link that might be useful: TAMU Tomato Problem Solver