case - installing a motherboard tips?

I have a couple questions regarding installation of a new motherboared. (FM2-A85XA-G65 to be exact) the case has a small metal stand-like thing in it, and though it needs a couple for screws one is sticking out where there will not be a screw,but unfortunately I can't seem to get it out of the case.I think it's made of copper because of the color. will this cause the motherboard to short out?

another thing, is that the PCIe ports inexplicably don't line up with the back. will they still be usable or do I need to buy another case?

my last question, is whether I need to buy thermal paste and how much of it I need. I am installing A8-6600k.

edit: thank you for your feed back. I'll make sure not to ask so much in one thread next time. I noticed that the ports nor the bracket are centered in the center of the PCIe, but are actually offset by so much the the port only marks the beginning of said card. I have bought some thermal paste to be safe,as I'm unsure whether the cooler has any.

the case has a small metal stand-like thing in it, and though it needs a couple for screws one is sticking out where there will not be a screw,but unfortunately I can't seem to get it out of the case.I think it's made of copper because of the color. will this cause the motherboard to short out?

Yes, you should (have to) remove any standoffs (brass in your case) that doesn't match the MB's mounting holes. It is very likely that you can experience an issue in such scenario. it doesn't have to be fatal issue, but it can prevent your MB to work properly in best case. Most motherboards usually have SMD elements mounted at the chipset area on the back of the MB, so the standoff may cause the physical damage as well, if it puts the pressure on these.

another thing, is that the PCIe ports inexplicably don't line up with the back. will they still be usable or do I need to buy another case?

Have you tried mounting your VGA? I don't think that you will have the problem. Never had such issue and I mounted thousands 'till today. The slot should be displaced and middle line of the slot should bi approximately lined up with the top edge of the PCIe-slot back-panel opening.

my last question, is whether I need to buy thermal paste and how much of it I need. I am installing A8-6600k.

Regardless of the CPU type, you MUST have thermal grease applied. You need it a very little, so if you can borrow from someone, don't buy it. Even the smallest syringe (~3 gram) is sufficient for 5 to 10 large CPUs

Edit: @blubberdiblub - Your part about the NEW CPU with a stock cooler is perfectly correct

I recommend removing the stand-off, if possible. It could short-circuit or damage the motherboard. But also check the bottom side of your motherboard. Many motherboards have a circular patch of copper or a drawn circle in a place where they expect you to provide a stand-off, but without a drill hole for a bolt, in order to support the board and prevent it from bending too much when inserting new RAM or Expansion Cards - often near the PCI Express slots.

For the PCI Express slots, do you have an expansion card to verify that they are actually misaligned? Maybe you only think they are? Imagine the PCB of an expansion card - which goes into the slot - and the slot plate, which is fitted to the PCB in a 90 degree angle into one direction (not centered on the PCB of the card) - which fits into the opening - and thus the center of the opening is not on the imaginary extended line of the slot.

Usual retail CPUs come with a cooler that already has thermal conducting compound applied to it. It's fine to use that if you're going with the standard cooler and you shouldn't apply extra paste to it.

If you plan using a different cooler that has no thermal compound preapplied, then you need thermal paste. It's recommended to watch some youtube videos like https://www.youtube.com/watch?v=-hNgFNH7zhQ on how to correctly apply the paste - regarding amount and shape.