I promised, sometime ago, that I would pause and reflect on my experiences of constructing a bike from scratch. I think I am going to split this into sections, mechanical, philosophy and riding.
What you do have to be careful of is mixing and matching components. Some gear shifters don't work with some mechs. Some bottom brackets don't fit some frames and also need different tools. Wheel hubs will only accept certain sizes of cassettes. Even the frames have different capacities that affect headsets and wheel/tyre choice. All in all the idea of just picking things up in a random fashion is not a good idea. From a mechanical stand point, I'd suggest a list of choices, and a little research. Being a blind bike builder can be a slow and expensive process.
Start off with an idea of what you are going to use the bike for and develop that. There are no rules that say what you initially put on the road/trail is the finished article, so don't hold out for the ultimate kit if you can get hold of an alternative that will get you out riding sooner. Parts will always need replacing, and I missed being able to ride when I had taken both bikes off the trail.
As you develop the idea of what you need the bike for, a certain frame type and gear/wheel combinations follow on. Be guided by the price of components. Put the higher priced ones as the guide for getting the rest that are dependent on that.
Mechanical assembly is pretty straight forward. A bike is after all a bit of pre-fabricated engineering. Most bikes are developed to be relatively simple to assemble and parts in general fit a logical scheme. Whilst a generic understanding of how a bike fits together is important, either through analysis of an existing bike as a template or through experience, most of the build is suggested by location. Bolt front wheel to front axle, rear derailleur to rear stays on the right is not exactly rocket science.
Finally, what you don't know you can find out. I tried to do most of this build without to much reference to the internet and books, relying instead on my abilities to analyse a system and understand how it works. Having said that "Zinn and the art of mountain bike maintaince" was invaluable for checking my logic. If you get stuck and you need a practical demonstration then the Bicycle Tutor has excellent "how to " videos. Other riders were also helpful sources for ideas, although not always correct. You can find all sorts of conflicting advice on bike forums, based on conjecture and one off experience, they will give you an idea but don't take them as gospel. Instead, go to Sheldon Brown who has compiled lists of technical information in a much more rigourous manner.