First of all, welcome to the club. I don't know that I can address your specific issues, but I will say that my initial experience with this game was a little love-hate. I bought mine from a friend last year who took excellent care of all his pins, and had done a lot with his JP. When I bought it I had a side-to-side movement T-Rex issue and a couple of other little things. It took a little time, but I got them all worked out and ended up even doing several mods and customizations.
Be patient and you'll get things worked out. The group here has been really helpful to me, and I'm sure those with knowledge will give you some direction. I think the ball trough issue may be a fairly common one that others have experienced, and I'm wondering if the sound is related. For example, if a certain switch triggers that sound and it is stuck/faulty or something then that sound me be continuously triggered until a subsequent event occurs.
If you run a switch test, what errors (if any) are you receiving?