Is it possible to customize the email notification header with a different color?

Also when you open it the light grey header above the information  has your name JotForm in black and orange is there anyway to customize that area with a different color and or the name of the client site so it appears the form is the clients form and not a Jot form?

I believe you are talking about the light grey bar in the header of your email notification.

From there you can pretty much modify it as you would like using the toolbar at the top of your email notification template. If you want to make more advanced changes then this can be done using the included html button.