i'll try to answer in order:
bent pin - in general this is not a god thing but you will not know if it caused a problem until you actually try the cpu
pads on the corners - they are supposed to be there,
do not remove them. they are there to keep the heatsink from crushing the cpu core and it keeps the heatsink level, without tilting to a side/corner
arctic silver application - first, since you are using arctic silver (and it is good stuff), you must completely remove the pink pad (the gum like stuff) on the bottom of your heatsink (it is possible it didn't come with that pad, but it probably did). basically, you want to apply a very thin, even layer on the cpu core. if you apply it too thick it will act as an insulator (that's bad).
here are the instructions from arctic silver themselves...