On the diet, of course Vitamin D typically is not greatly present in food and the sun is the main natural source.
Unless you use iodized salt, the iodine is of course a disaster. It's entirely possible to have a diet that provides ample iodine, for example by regularly having plenty of dairy, baked potatoes with skins, seafood, or turkey. But typically people do not consume enough of these foods to provide ample iodine, so iodized salt use or supplementation is necessary.
For Vitamin E, the richest sources of gamma tocopherol (which the above program likely does not count as being worth much if anything towards the RDA) are pistachios and corn, with amaranth, blueberries, and walnuts being moderate sources, and all kinds of things providing still-significant amounts. You might well have a good amount already, just not shown by the program. For alpha tocopherol, which the program absolutely will count, sunflower seeds and almonds are the richest sources.
For reason of balancing benefits of those nutrients versus it usually being undesirable to add to linoleic acid intake, among those I'd pick pistachios, almonds, and corn as potential Vitamin E sources.
On Omega-3, unfortunately the program does not distinguish between DHA, EPA, and ALA, so your amount of DHA is likely considerably less than the total given by the program. At least in terms of diet man has been adapted to over the long term (such as 100,000 years) the corresponding amounts of DHA, EPA, and ALA would be far higher than in your present diet.