First Build Case and Mobo Issues

I'm building my second PC and have been using tek syndicate's youtube video as a guide. The build is almost complete with just 3 things standing in the way:

I have been having trouble with my mobo, the MSI H81M-P33 Micro ATX LGA1150. It doesn't have enough "pins" available and there is no USB 3.0 port. By pins I mean the square and hexagon plugs that come in 6s or 8s coming from the psu, which I need to plug in my cpu.

The other problem I've been having is that my gpu doesn't seem to fit in my case. The ledge where you screw down the graphics card is outside the case for some reason, so the graphics card doesn't have a ledge to sit on, and won't go flush with the case. This leaves the port it's supposed to be plugged into unusable.

My question being: Is there anybody else who experienced these problems and found a work-around or notices that I am missing some really obvious thing? Otherwise, is the only solution to return my components and buy new ones?

If it helps, a list of components can be found here http://ca.pcpartpicker.com/p/JQbxK8

Id make sure that yo are using the right cable for the appropriate component as the wrong cable can do tons of bad things plugged into the wrong place. Since this post is 6 Days old, not sure if you still need help or but here is my input. From the looks fo the case there seems to be a small panel you need to unscrew from the ouside that will allow you to screw down the GPU. Pretty sure that that is holding down the PCI slot covers and undo the probably one screw and it should pop off and the GPU should slide in.

Check to make sure your matching up the power connectors from the PSU to Mobo correctly. It looks like your MSI board has a 4-pin power connector for your CPU, as well as the standard 24 pin connector.

http://www.playtool.com/pages/psuconnectors/connectors.html

The GPU should fit in the PCI-E slot, just take your time with the case and make sure your assembling things right.

If you have further issues, post pictures.

6 pin or 6+2 pin power connectors are gpu power connectors, and those are not ment for the cpu, they are slightly diffrent aswell, and should also not fit in the cpu power socket on the motherboard.

check the manual of the psu, which powerplug is for cpu power.
in your case you need a 4 pin powerplug.
Mostly there are two 4 pin cpu power plugs, but some psuĀ“s also offer both dual 4 pin and single 8 pin cpu power plugs.

I might also mention that since this is your first build you may or may not know that not every plug or wire from your PSU will be used, just make sure (read the manual) that all the connections are made to your mother board and graphics card with the appropriate cable from your power supply, you will have cables coming from the PSU that you will not use because most PSUs are made to work in a variety of different combinations of motherboards, cpus, and graphics cards.

The CPU power connector should be in 4 pin format as the 6+2 pin connectors are for graphics cards. The 24 pin connector is the motherboard power connector.

I haven't ever heard of a motherboard having a direct USB 3.0 port. Perhaps you are confusing the USB headers for actual USB ports.