Okay, I was up late last night doing some more work on installing the computer.
I reoriented the motherboard, and then all of a sudden, things just started dropping together. I was able to set everything up so that not only is there a ton of airflow, but I can easily open and close the CD tray (which was a previous concern). Right now it's an absolute rat's nest of wires, mostly because of the front panel mount. I ordered some organizational supplies from the store, they should be in next teusday and will make this rat's nest look 100 times better. I did get curious and plugged it in...
IT POSTS!
Both drives were read, the panel mount even worked when I displayed the BIOS on my downstairs TV. Not only that, I left it idle for an hour, my temperatures floated around 65 degrees F, about 20 or so C. I'm really really excited about that.
The motherboard is on "stilts", actually, the sides are mounted on the one-by-ones and I used threaded posts and flat flanged T-nuts to make a support of sorts so the entire thing is sturdy as a rock. The room underneath also makes for plenty of airflow.
I made a mounting bracket of sorts for the CD drive and hard drive by using some stuff lying around the store.
Ignore the mess, it will be alievated soon, but incase you were curious of how it looks right now.
Thanks guys.