My motherboard is misaligned to the case stand-offs, and is on a sloped angle?

This is my first PC build. When installing the motherboard (MSI B760 GAMING PLUS WIFI) onto my case (DEEPCOOL CC560), I noticed with the IO Shield installed, the motherboard will just not have more than three stand-off holes aligned. Taking the IO Shield off, the motherboard slid into all the holes, but I noticed the top of the motherboard was higher than the rest, and that there was a slight misalignment.

This is the only motherboard I have at my local store, so should I return it, or just roll without an IO shield?

If I were to return it, how do I get the thermal paste off of the CPU..?