"The video card I'm going to get is PCI Express 2.1
But my motherboard has PCI express 2.0. will my video card work in it? "
Yes. The card is backwards compatible.
"The case says it has a panel for USB 2.0. Will that work for USB 3.0?"
No. You need a case which specifically states USB 3 on the front panel. Look for a different case.