Look into the Topeak multi-tools, you'll find a basic one with a screwdriver and the allen keys you'll need. It will be more compact than separate tools. It seems most people won't mess with a seat wedge but I'd probably take the multitool out if leaving the rest on the bike. A road morph pump will give you leverage like a floor pump so its much easier to inflate tires to full pressure than with a mini pump. They come with clips to attach it to the frame.

A patch kit should cost you about $3, its just some patches, glue and a bit of sandpaper to rough things up. I find the Zefal ones work well.

Not on your list but I'd highly recommend for commuting is a rearview mirror (take-a-look)