I don't find the padded short necessary for comfort on a single day's ride. Basically, if I'm going to spend all day in the saddle, I'm probably going to finish the day a little sore no matter what I wear. What I like is that the padded shorts can change the pressure points. I will generally have one pair of padded undershorts in rotation, and will rotate them in every couple of days. That way if I'm a little sore from riding the day before, I won't hop on the bike and aggravate the same spots.
On footwear: I've been riding with Swiftater Crocs all summer. I do like them, but I recently picked up a new pair of Newport H2s. I've had them before and loved them, but I've had longevity issues. We'll see if this pair does the trick.