I have never built a shop from scratch, however I have been working on a complete renovation of a 3200 sq ft shop (I am almost finished). My advice is spent alot of time planning on how you are going to use each area and make sure you have plenty of electrical/lighting. It is much easier/cheaper to overdue it when it is being built, rather than wish you had it later on.
Also, build it as big as your zoning/budget will allow. No matter how big the shop, you will still find ways to fill it up.
I used a program called SmartDraw to help layout my shop. It seemed pretty easy to use, they have a free trial (I think 30 days), but I liked it enough to buy it. It was a huge help in for all the planning.
Good luck with your build.