Hello, Julian,
The green opto board carries the infra-red l.e.d's, which are (or should be) continually 'lit' from the 12v and Ground wires which supply all the machines' opto light sources. It looks as if an attempt's been made to improve on the original idc connector. I've seen worse; a supposedly top-notch operating company traded in a Star Trek Next Gen with the resistors on that board removed in favour of some mounted on a piece of tagboard nearby. Maybe they were on to something, though - broken resistors were so common that Williams changed to remotely-fitted resistors not long afterwards.
As Andy says, Trough 1 & 2 are a frequent false error on games that don't often use all six balls at once. Indiana Jones PBA avoids it using the Well of Souls mode, and Star Trek keeps three out under the playfield in any case, but Popeye f'r instance only has two* cases where the trough goes empty (the final wizard mode and a special case involving the 4-ball Animal multiball.
Btw, the pictures show a fixing screw missing from the opto board
* that I could think of until I thought of Item multi-ball. As with Animal m/ball, starting this 4-ball mode with two 'regular' locks made sees the trough emptied to serve 4 balls in play
