drives-could be after card, but looks like theyd be out of the way
mobo- maybe with CPU,HS and ram already on
that other crap if not done before installing mobo
PSU last. why deal with the wires before you have to? also helps with routing this way.
1) As per the instructions, a dot the size of a grain of rice is sufficient. Some folks even smear this to give better coverage before you put on the heat sink.
2) IMHO, I will usually assemble the items out of the case, connect the PSU and power it all up, just to get an initial test before I go through all the work of assembling the box. If everything powers up to BIOS, so much the better. On some builds (such as when I am water cooling), I go so far as to load the OS and burn the machine in before I do the final assembly, to be sure I don't have any leaks, which can be hard to spot inside the case.
As far as BIOS adjustments, I always go in and turn off any device on the planar that I am not planning on using (ie, onboard sound, video, etc.) to free up resources. I also check to see if there are any BIOS flashes that I might need to apply before I install the OS (an absolute MUST if you are installing any flavor of Linux). If I am planning on overclocking, I will adjust the voltages to norm for the chipset rather than rely on the default settings, and then eventually tune the voltage down until I reach stability once I have reached my desired overclock. And a lot of this happens before I put anythign in the box.
When you are assembling, it helps to have a removable motherboard tray. DO a dry fit with your PSU, hard drive, optical drives and any peripherals (ie, card readers, front panel USB and sound, etc.) to get a feel for how long your cable runs will need to be, and then add a couple inches. Get out a Sharpie and mark where you need to place you cable-tie standoffs. After that, install your motherboard, then fit in your drives and finally your PSU. Go through and make your cable runs using cable ties to the standoffs you placed earlier. The more you can get cabling out of the way, the better your airflow. It is time consuming, but if you are meticulous at this stage, you will be the envy of your mod club later for your attention to detail and the "clean" look and feel of your build.
If you are unsure of the voltage settings, then the best advice I can give is to let your BIOS assign those values. If you don't know what you are doing when you change the voltage settings, you could very well brick your system and end up having to replace your processor, memory, motherboard, or all the above. Such is the risk you take when you are overclocking.
When you have read up a lot more on core voltage and understand the ratios and the expected tolerances of your CPU and chipset, then it might be fun to try and squeeze every last bit of performance out of your system. Also, for your freshman efforts, I recommend you work on a system that you won't mind melting down into a brick if you should do something wrong.