Thank you for the help so far, sirs.

After much trepidation, I fired the new rig up today. No fire or even smoke was seen - so far.

There are a few issues that require your esteemed help:
.............................
.............
The handbook for the motherboard suggests if only 2 memory sticks are used, they should be placed at the 2nd and 4th slots.
"Enabling Dual Channel Mode can enhance system performance."
Now, how do I enable
dual channel mode or is it automatic? The alternating slot placement works for me because the memory sticks have large heat spreaders, which prohibit me from using slot 1 anyway. The CPU cooler partially blocks the first slot.
.............................
............
Again regarding the memory, how do I go about changing the settings or at least confirming the motherboard is running them at the manufacturer's recommended timing?
.............................
.............
Tested the "rate system performance" thingy in the control panel but the graphics came up rated 1.0. How do I make sure the video card is running the graphics and not the onboard chip?
.............................
..........
The system has 5 fans: CPU, front, front, top and back. The top fan and lower front fan do not turn on. I tried to find out why but the MSI motherboard utility only lists three fans. The utility says sys1 fan and sys2 fan are on auto settings and working fine but those numbers don't correspond with the fan numbers on the motherboard:
Sys1 fan - hooked to top fan (not working)
Sys2 fan - hooked to bottom front fan (not working)
Sys3 fan - hooked to top front fan (working)
Sys4 fan - hooked to back fan (working)
CPU fan - hooked to cpu fan (working -thank God)
.............................
.........
Finally a question on temperatures. The CPU temp goes from 32 celcius to 34 celcius and the motherboard seems steady at 26 celcius. Are these normal ballpark numbers? I assume the non-functioning fans would help a little bit, but these temps are without any programs running.
My system is an i-5 3570k in an Antec900 case with a Hyper212 cpu cooler.