Maybe I'm not the norm when it comes to Mac users, but I actually do use PCs and Macs, and have a low power box I threw together under my desk running Linux just getting used as network storage.
First, cards don't have pins. They are printed circuit boards with contacts that slide into slots, just like RAM.
Onto the building part. You can't install stuff wrong. It is the square peg, round hole situation. The only part that is possible to screw up is the processor because the pins aren't meant to take any
abuse, but it should be very clear which way they go in. Unbending the pins is impossible. I personally prefer the land grid array layout(LGA) that Intel has been using with the pins on the motherboard, and the large "clip" that fits over the processor before putting the heat sink on. Pin grid array(PGA) stuff had the bad habit of the processor getting pulled out of the socket when trying to remove just the heat sink, and the release bar is covered by the heat sink so you can't carefully pop the processor out.
Everything is labeled, and stuff only goes in 1 place. 4 pin power by CPU, 24 pin(20 on older stuff) only has one possible place to go and nothing else looks even remotely like it. The PCI-e graphics card will only fit in a 16 lane(physical, which doesn't necessarily mean there are 16 lanes electrically) pci-e slot. The only other connectors are USB(which only goes in 1 way (one row as 4 pins, and the second row has 5 while one row of the connector has 4 holes, and the second 1 has 5), power and reset buttons, LEDs, and some times IEEE1394(firewire) which is a pain because it isn't one nice cable like USB is, and you actually need to read what connector goes where).
Other than that, common sense dictates that power supplies have all those cables coming out of them for a reason. You don't want to be running every peripheral off one rail. Balance the load across all those separate cables with the molex and SATA connectors for peripherals.
Make sure none of the silicon is touching the metal on the case.
Uhh... what? The only silicon is inside the packaging of the integrated circuits. It physically isn't possible to have silicon touching anything it isn't meant to touch unless you cracked open ceramic casings of stuff. Do you mean the printed circuit board?
The only thing I would suggest that isn't either self-explanatory, or necessarily a common sense thing is to clean the thermal paste that comes on the heatsink off using isopropyl alcohol, and apply some Arctic Silver(or similar). Between using MUCH less of it than the amount that comes on the heatsinks, and it being less sticky, it makes pulling off the heatsink easier, and as an added bonus, it keeps your processor a few degrees cooler.