My big decision is Intel or AMD? Suggestions?
Depends upon your budget and performance requirements. Here's my general rule:
Performance: Intel Core i7 9xx
Budget: Intel Core i5 or AMD Phenom
When I built my system a couple years ago, I went with AMD since the i7's were insanely expensive and the Phenoms were the next-best processor at a MUCH lower price. I think these days, the i5s and Phenoms are roughly the same price (it's been a while since I've looked at processor prices). Also, spend some time learning about the different motherboards. There are vast differences between different mobo's that are designed to support a given processor type.
Also agree that you should forget the on-board graphics and go with a separate board. You have the option of going cheap\reliable to crazy-fast and expensive.
And I agree with Pat, be sure to go SSD for the boot drive. The boot speeds will amaze you and they are roughly the price of a good hard drive these days.