Go with custom, you'll definitely get more for the money. It doesn't takes a rocket science to put a computer together, everything is like plug and play.
Plus most hardware you buy, will comes with 2-3-5 years warranty from manufacture, and you can upgrade along the way.
Brands to go with
Motherboard: MSI, EVGA, ASUS, Gigabyte.
VideoCard: MSI, EVGA, ASUS, Gigabyte, Galaxy, XFX <--- gonna love their life time warranty.
Powersupply: Seasonic, Corsair, Coolermaster, EVGA
SSD: Sandisk, Samsung, Intel, crucial
RAM: Muskin, Kingston, Crucial, G.skill, Patriot,
Everything else is just personal preference.