Oh boy, he really did leave you with a mess. Woulda been nice if he had tagged all those connectors for you beforehand. I'm afraid troubleshooting this over the internet isn't going to be very fruitful as there's a lot of little things to miss. Know any cobalt people around there? Even having someone else's car to look at would be helpful.
Picture 1 an 2 looks like there is a connector that matches there but I couldn't tell you where that goes.
Picture 3 you are holding what looks like 2 ends of an o2 connector, the ones with 4 pins and a blue safety line on them.
The metal thing in your hand looks like the bleed point for the clutch, that needs to go back on the transmission. Also looks like it's missing the C clip that holds it onto the transmission nipple and the one that holds the clutch line.