1 -There are a lot of cables (5) touching the motherboard because of strange placement of case holes. Is it bad for cables to touch the motherboard?
No, as long as they're not touching something that gets hot and they're not plugged into anything.
2 -The modular PSU I have had 2 cables that aren't removable but one of those cables is a 4 prong and for the life of me I couldn't find out where to plug it in. (The PC works, OS and everything... but that unplugged cable bothers me a bit lol)
That's probably the 12V line for the processor. As long as you have at least a 4-prong plug to the 12V-EXT (or whatever that's called ) line, your processor will work fine.
3 -Usb 3.0 header that runs from the top front of the case won't plug in anywhere so I can't use the usb 3.0 on the front of the case. Is there an adapter or something? The motherboard had usb 3.0 on it so I have 3.0 from the back.
If you mean your motherboard doesn't have a header for the front panel USB3.0, you can get USB3.0 to USB2.0 adapters, like http://www.pugetsystems.com/store/item. ... m=d41d8cd9
4 -My motherboard didn't come with a speaker so I got no post beep. (again, it seems to all be working but no post beep!) Since the OS is up and running, everything seems to be recognized do I need a post beep?
Only if your computer doesn't even get to the POST screen. But you only come across this if your hardware fails.
5 -All 3 case fans have small 3 prong plugs (small new ones) while my PSU had larger molex so I had to plug all 3 of my case fans into the motherboard. I've read this is bad because it
takes power or processing away from the motherboard or something?
This is fine, whoever told you that doesn't know how to electrical engineer. Well, the only time this would be a problem is if you're on the teetering edge of how much power the PSU can provide. But fans draw so little power, if you're at that point, your system's going to go unstable.
6 -One of the motherboard power cables (smaller one) is touching the graphics card. It that ok? (you can see in the picture how I had to run it inside of the case in front of the GPU.
I don't see a picture. But as long as no metal is touching, then nothing's going to happen.
7 -I also simply inserted the Windows disc and never chose what the PC should boot from so now when I turn the PC it searches other places before the HDD. How do I fix this? My TV I have it hooked to shows in a big in the way box "you have selected HDMI" and blocks the text "press ....... ................." when it first boots so that I can't see what I need to press. I don't have a monitor.
Go in your BIOS settings and change the boot order of the devices. I don't know what BIOS you have, but there should be something in there for boot order.
For your cables, I would get some zip ties and bundle up the unused cables and tie them together.