It goes from that gold/orange color to a deep purple color. MJ has the coolest finished Ive seen on a guitar by far. Its also cool to see people who have never seen an MJ look at it. The tuners take a little getting use to, but it doesnt take long. As Elberfan says, they will build you whatever you can dream up. I believe the Custom also comes with Humbuckers.
My MJ is a relatively early one...built in 99. I believe they were still using Mahogany bodies on all of them at that point before they went over to poplar. I could be wrong on that though. Love the guitar though! It was 10 years of searching to find it.