I definitely agree with horizon. Joysticks should
not be diagonal. Players adjust to it very easily if not naturally.
As for the trackball, it kind of depends on how important Golden Tee, and similar games, are to you. I you are an avid fan of those, you might want to open it up. If not, are you willing to sacrifice a little playing skill to compensate for the extra controls.
Here's a shot of my control panel. It's 48"x20.75"

On my control panel, I don't have problems with hitting the joysticks while using the trackball, including while playing Golden Tee. I admit, however, that I don't excel at Golden Tee -- possibly because my movement is limited or I just haven't put the effort into playing it.
As AzureKnight was alluding to, mock-up your panel from the bottom side as well to make sure that all your parts are going to fit in your panel. The track ball mounting plate is huge, as well as the trackball enclosure beneath it.
Lastly, think about ergonomics. I personally would rotate your button sets unless you are going out of your way to let a person be able to choose to use their left or right hand for buttons vs joysticks on players 1 & 2. One thing I learned when re-making my panel is that the button sets were close to the joysticks. The configuration like you have, and I did, causes the player to keep their wrists close together and then twisted back in order to stay in proper orientation with the controls. For instance, your position of your dual player joysticks will be natural for your arms as they will probably be shoulder length apart and your arms will be perpendicular to the screen like this
| |. While using the joystick and button set, your arms will make the shape of a
^ with your wrists twisting back to to line up best with the button orientation. This is, by no means, ergonomic and will wear you out over long usage. In my configuration above, the button set is rotated to allow the left arm to stay perpendicular to the screen and the right arm rotated in a little to the left. My arms are effectively in this orientation
| \, but more importantly neither of my wrists are twisted which makes it much more comfortable to play.
If you want the Visio file of my panel, let me know and I will send it off to you. Good Luck!