You won't be able to use the front headers at all. Not unless it has 2.0 and 3.0. In that case the 3.0 wouldn't work, but the 2.0 would still come with a viable connector.
It is a bad PSU, but the system isn't really being over taxed. You're hitting with max draw around 70% of your max Wattage (4790k 88W + 980 TI 250W + 40-60W for storage) 400ish W out of 550W. Regardless if you have the $$ I would upgrade to a nice 600Watt 80+ Gold. Play it safe.
He has a http://ark.intel.com/products/36526/Intel-82Q43-Graphics-and-Memory-Controller-Hub that has a PCIe Gen 1x16 in there, so you could get by. 750TI would be nice I just don't know how your system will handle the power. They do have SFF PSU's you can throw in there, but they're expensive to...
Don't use the autodetect then. The bar right next to it will have your drivers. Just click download on it for the proper operating system and 32/64 bit.
Go with Srimasis' build so far, I would get 2x4GB memory to use the bandwidth from dual channel. I would save some money on the 960 and just get the 2GB version since it can't even max out the 2GB VRAM it does have on its bus.
You don't have a MiniDisplay/Thunderbolt port on that chassis from what I can find online, so I would have to inform you that you won't be able to use a product like the Razer Core.
Start menu isn’t working
Here’s how to fix one of my favorite Windows 10 error messages: “Critical Error/Your Start Menu isn’t working. We’ll try to fix it the next time you sign in.” You may also see the error, “Critical Error/Start menu and Cortana aren’t working. We’ll try to fix it the next...
I wouldn't use XP because it's no longer supported, but your system seems like it'd be held back by windows 7. Kind of in a pickle. If you can slap 2 more gigs of RAM in there I'd say you're set. Hope this helps.