The drop targets falling when they shouldn't might be due to the solenoid expander board under the left side of the playfield. There's a lamp right next to it that's part of the solenoid expander activation circuit. Put the game in lamp test mode. If that lamp isn't flashing, replace it. Otherwise remove the solenoid expander board and reflow any bad solder joints you see.

From memory, switch 41 is a single switch in the middle of the zipper flippers and comes up closed in the switch test when the zipper flippers are wide open. Lift the playfield and manually activate the coil that pulls in the zipper flippers and see if #41 stops blinking in switch test mode.
The Bally switch test mode only shows you the lowest number switch that's closed. So if all switches 41 through to 48 are closed, the switch test will only report switch #41. Coincidentally the seven upper drop targets are switches 42-48 so until you open switch 41, you won't see the drop targets switches in the switch test.

Oh yes looking at the schematic, I see what you mean. It will be the diodes on the coils you see with one leg connected to either a brown/orange wire or a grey/red wire that might be shorted.

Well done

These Bally flipper cranks look pretty close to me:

http://www.marcospecialties.com/pinball-parts/A-1889-7
http://www.marcospecialties.com/pinball-parts/A-1889-8

The cranks on my zipper flippers are horribly worn because of metal to metal wear at the plunger pivot. I haven't investigated it yet but I'd like to see if any traditional crank and plunger rod with link from that era can be used instead.