If you run it on the BOX it will prevent any possible shorts in the case.
All you need to do is put the board on the box and install CPU and cooler,video card,memory, PSU and boot into Bios and see if all the ram shows up.
Just take a paper clip touch the 2 power pins to power up, unless the board has a power up button.
Also look at the bottom of you CPU and see if there is anything wrong with the conductive pad.
Also look at the CPU socket and see if there are any bent pins.
You are fantastic! I got a bit busy so it took me couple days to tear it all apart again. I did as you suggest, after I clean the CPU of the thermal glue I went on to clean the cooler contact as well then applied a smaller pea size amount, while it was out of the case I did exactly as you suggested only I started out with just the one stick in Dimm A1 and from outside the chassis, no problem with the dimm that's been the problem so I place the board back in the thermaltake chassis and couldn't get it to post. After trying a in and out the chassis a few times I just laid some lightweight packing paper against the back wall of the chassis put the board in and problem solved. I added ram one at a time, rebooting each time I added one and every time it was successful. Thanks so much for your help, I now have all 16 gig on the board up and running. You're a gem.
What a nightmare for your first build.