I built mine a few months ago. The biggest thing that came up for me was information overload. Like you, I wanted to build a PC that will last a little while and has some upgradability. In my research, I read forums, product reviews, and tried to get a sense on what the future will bring. A lot of information, and I got bogged down in a lot of specifics.
A note on manuals. What ever you decide on, the manuals on some items are fairly complete, but again its easy to overlook a step or two, and you find your self backtracking. As Norm Abrams would say, "Know your power tools, read and understand..." This apples to PC components as well.
I made 2 mistakes in my build. The first was getting a dual core instead of a quad. FSX really shines with multiple cores, and I didn't do enough research on that aspect before purchasing. I rectified that by getting the qx9650, but that brings me the second mistake. Don't overlook proper cooling. I just purchased a decent CPU cooler from Noctua, as the stock cooler just doesn't cut it. Especially if you overclock.
Cable management can be difficult depending on you case and components. Good luck.
My best advice - Be Patient.