The cable routing for the motherboard connector is weird. Be sure to route the cable attached to the logic board connector so it doesn't go into the battery compartment. Before taking out your headphone connector, take a picture of the cabling so you can figure out how to fold the cable so it's at least flush. Don't stick anything down until everything is in place, because you'll be adjusting the cable as you go.
Don't put the mute switch in first - the cable is to bendy, and it'll go everywhere. Screw the volume buttons in first, which'll allow you to position the mute switch and make it stay. You can use a Q-tip or something to make sure that the mute button assembly stays in place while you screw in the screw.
For the mute assembly, the hooked part of the shield goes towards the top of the phone.
Note that the adhesive on the iFixit cable is bad, and doesn't really stick so well.
I had part left over, a right angle part with a screw hole in one arm and adhesive pad in the corner. Odd.
The clip actually looks like it might be a ground. it's gold and is folded in two. There's a screw cutout and something that looks like it physically is supposed to touch something. Phone works fine without it, though.