I'm not familiar with JD, but these problems you are experiencing are most likely related to a malfunctioning switch. Easiest way to do this is to have the manual handy, or a printout of the switch matrix, and locate the switch you think is causing the issue. This is the "Switch edge Test". You can toggle through each switch on the playfield, and it will tell you what was the last switch. Test the switch you think is faulty.

The other thing to check is that after 10 games ( I think it is 10 games), a switch error will appear during diagnostics or boot up - this will point you to the switch

In addition to what Nino suggested, with the OPTO's you should be able to break the beam with your finger (wont hurt I promise!).  When you break it, it should register on the DMD.