Best advice is to get it built custom, definitely. You usually save the overhead of buying a big name brand, plus can tune the thing to your needs. Reusing cases and peripherals is also a plus to keep down costs. It's what I've done for many years... the only true skill is to hunt for bargains on
NewEgg for parts in the end. Great service and actually useful user reviews!

Try to target mid-high end parts on sale as a better thing replaces them or now you might be able to catch a summer or back to school special later on.
Also, if you are open to try out some open-box or factory refurbished items, there's a good bunch of sites out there to make your money go farther. Prices are coming down quickly lately in second-hand, especially for laptops.
TechForLess is a site I have dealt with in the past for refurbished and reconditioned electronics and they have not let me down so far... get on their mailing list and you can get access to even bigger discounts.
Hmm.. that almost sounded like a plug.
