If you're starting to get up to riding an hour at a time, you can get a good benefit from both clipless pedals and cycling shoes. I think you will actually get more benefit from the shoes than the pedals. I think you will also find that clipless is a lot easier to deal with than toe clips. I'd suggest spd mountain-bike style cleats and shoes, since they have a flat sole and can be walked around in.

Shorts make a big difference in comfort. You can find ones that look like normal shorts but have bike shorts inside if you don't like the look of spandex.