Your case does support: Micro ATX / ATX. The reason for the standoffs and this: Rule of thumb: one standoff for each motherboard screw...no more, no less. ...is for physical support of the motherboard. It keeps the motherboard from "flexing" when you install things like RAM, vid cards, CPU coolers, etc. "Flexing" a motherboard too much can crack/break the tiny circuit runs in a motherboard, which will kill the motherboard.
As for the drivers, it always best to use the motherboard CD that came with the motherboard. Then, if any problems arise, try the newer drivers on the manufacturer's website.
Microsoft is very busy trying to force everyone to use Windows 10. They've even gone so far as to pay manufacturer's to make Win 7 drivers, hard if not impossible to find.
As to the power supply, it is supposed to be installed with the fan pointing down, if your case has air holes underneath. The reason for this, is that it doesn't starve the vid card for the airflow IT needs.
Generally the case air flow should be like this: Intake at front and bottom, exhaust at top and rear. This gives the
hot components like the CPU, the vid card, and the motherboard itself, plenty of airflow.
As for the hard drive noise, there are usually two reasons...
1. Bad hard drive. Which I do not believe is your issue.
2. Various mounting methods.
Most newer cases have the hard drives mounted on flexible trays, to prevent vibration...like this:

The hard drive LED should light, when w/e you are doing, is reading/writing to the hard drive. It's not a major thing, but can help sometimes. Once you get used to a build, excessive hard drive activity, may help to notify you of an infection or similar.
Last of all, when you buy a complete computer build (that includes a monitor) for $600...you should expect a few issues, or difficulties.
Glad it all worked out for you though. Might be a good idea to call Thermaltake and ask about the standoff issue. Sooner or later, having the motherboard NOT mounted properly, will result in "flexing" of the motherboard, as I mentioned above.