1) USB 3.0 - sounds like it is supposed to plug directly into the back of the motherboard? Either way if you don't need it you could leave it disconnected. Or if you are able, leave a PCI slot cover off (one that is not needed) so it can run out the back through there and connect it up, or going a step again you could manually drill a hole in one of the PCI slot covers so that it's just enough for the cable to fit through and still have it mostly covered up.
That's the only thing that makes sense, but at the same time doesn't make sense. Who builds a computer with an internal cord coming out the back of the case to be plugged in?
I've also encounter a (major) roadblock today. I was harvesting my old (current) PC for parts and apparently the disk drives don't have SATA connections. I knew the HDD was SATA and assumed the others did to, but the back of the DVD drives have a 40-pin ports. I looked into IDE/SATA adapters but it's (much) cheaper to buy DVD drives. Not much luck finding a SATA floppy, though, so I may just go without until I get a converter.
One of my Motherboards came with an extra USB and Fire wire bracket which would fit in a PCI outlet at the back of the PC, It has a female plug so would fit on pins on the Mobo or could be connected to a male socket.
You did make sure that the pre installed standoffs in the case matched exactly the screw holes in the motherboard and that there were no extra ones left over?
If one is left there it is the most common fault for a PC NOT to post as it causes a fault and the computer shuts down, usually within 1 or 2 seconds.
I did use most of the extra standoffs to fill in the holes that didn't have one. I have a couple left over, but all the screw-holes in the motherboard now have a standoff underneath them.