Saving money is great, but the real advantage of a custom build is making choices for you. Junkyard turbos can work great, but it's a bit of luck.
If you want a killer set-up, learn how to read and plot compressor maps.
There are some companies that don't have the resources to do the maps, so those should be chosen partly based on a similar combo that works.
Be realistic about your power goals, and above all, drive agood factory turbo car like a GTR or a 911TT so you have a reference of what it feels like when it's done right.
Then, if you are not a trained welder, use factory manifolds of some sort, that way any mistakes will not adversely affect the turbo.
Unobtainium Welding Exhaust
GPI VVT Turbo Cam-in