Well, after struggling to read through this post, I'm still not sure what the problem is. It sounds like something isn't hooked up right, but hard to tell.
I'd strip the whole thing down, take it all out of the case and put it all back in one piece at a time making sure everything is firmly connected and powered.
To be honest, and I mean no offense, but you don't seem to have the knowledge to build a system. I recommend you find someone who knows what they're doing and let them assemble the computer for you before something gets broken.