Starting with Problem 3. what does you soil need? What did a good, reliable soil test say about what that soils needs?
Problem 4. Depending on the weather your lawn needs about 1 inch of water per week and it is best to water enough at any one time to get that water deep into the soil, 6 to 8 inches down. But then hot and windy weather can cause moisture evaporation which can mean your lawn needs to be watered more often.
Problem 2. The grass will grow back, eventually. As a rule after about 6 weeks you could overseed although my experience is that the grass will be growing back on its own by then.
Problem 1. The presence of clover, most likely White Dutch Clover, indicates a protenial Nitrogen problem. A good, reliable soil test will help here because there are several things you need to know about what is in your soil to intelligently determine what to feed that soil.
What is the soil pH? What is the balance between Calcium and Magnesium?
What is the level of organic matter in the soil? Organic matter opens up clay soils so both nutrients and water are more readily available to plants and in sand it helps hold both nutrients and water in the soil so plants can utilize them.
Grasses need about 2 pounds of Nitrogen per 1,000 square feet per year to grow well. 1/2 of that can come from the grass clippings, so mulch mowing is one of the better things to do. How much more Nitrogen needs to be added only a good, reliable soil test can tell you. Too much Nitrogen is a waste of your money since the excess simply flows out and pollutes the ground water.

Thank you kimmsr I really appreciate your help!

A couple things though. It has been 6 weeks since the RoundUp incident and the grass is not growing in, but weeds are...so should I maybe just reseed?

Also, Do I remove the existing clover? Or will it go away when I get my soil in better shape? What do I do about the left over patches after removing it?

Also, what is the importance of knowing the balance between Ca and Mg?

Plants need both the Calcium and Magnesium to grow and they need it in balance. Too much of one will interfer with a plants ability to properly utilize the other just as a deficiency of one will prevent a plant from using the oher.
I have found that when the soil has sufficient Nitrogen the clover is less of a "problem", but then I grew up in a time when having clover in the lawn was considered a good thing.
As you have seen, these products that are supposed to kill off plants do not always do what they should, but the "weeds" you see growing probably are growing from seeds where as the grass roots need more time to grow back in. Overseeding can get the grass growing sooner.

Sacramento.

What kind of grass do you want to have. In Sacramento you can sometimes grow the cool season grasses like fescue and Kentucky bluegrass but southern grasses like bermuda and St Augustine are easier to deal with.

There are no great organic solutions to the weeds you have. You can try vinegar but that is non selective meaning it kills everything. Having said that, I've never seen it kill bermuda.

Check your watering system with tuna or cat food cans. Put several out and turn on your sprinklers. Time how long it takes to fill the cans. That's how long you want to water. Once you do that a couple times, then decide if that is the right amount for your conditions. It can be very hot and dry in Sacramento meaning you'll need to water more deeply.