I'd work on one problem at a time, because sometimes when you solve one problem it will solve other problems with the machine... I always try to solve the easiest problem first, so I'll try to troubleshoot the drop targets that do not score.

When a target is hit and drops, it will close its target switch and send power to an A relay switch and then to an E relay switch. In turn, power is sent to the D relay coil (50 point relay) or the E relay coil (500 point/add bonus relay). So, make sure all the target switches, and all the switches on the A relay and E relay are clean and adjusted properly. When the ball is in play, the E relay switch with the yellow wire and the slate/white wire should be in the normally closed (NC) position.

Also, confirm that the D relay and E relay are working by pushing in on each relay to see if they will advance the score reels. And check all the infamous Jones plugs to make sure they are clean and seated tightly... And, finally, check score motor switch 1C (red/white wire and white/orange wire), since this is the main gateway switch that sends power to the drop targets...

For the target scoring and the bottom rollovers, you'll need to check the following relay switches:

A relay switches
D relay switches
E relay switches
G relay switches

Make sure all these switches are clean and adjusted properly. Also, make sure the switch stack screws are tight. And check the playfield Jones plugs that plug into the main board - see if the plugs are clean and properly seated...

Power to the E relay coil comes from the following playfield switches:

#1 Top Rollover
Right Target
Right Side Rollover
Left Return Rollover
#3 Top Rollover
Left Target
Left Side Rollover
Right Return Rollover

When one of those switches is closed, power will be sent to a "gateway" switch, which would be a switch on the A relay that sends the power to either the E relay coil directly or to the G relay coil via additional switches in that circuit. The playfield switches would "interrupt" power flow to the relay coils.

The following playfield switches will send power "directly" to the E relay coil:

J Relay Switch (Ball Kicker Relay Switch)
#2 Top Rollover
Right Bottom Outside Rollover
Left Bottom Outside Rollover