Your GI problem is definitely that connector. That's a typical failure. I've had to repair the GI connector on 6 of my games. The problem is that connector was rated for a lower amperage/heat rating then it would have drawn in arcades with the game being left on for hours and hours at a time.
As for repairing it, the good news is that the parts are cheap (the whole process costs about $5). The bad news is that it requires wire stripping, crimping, and soldering on a new header (what the connector goes into on the circuit board). You might want to have a tech come do this for you, or we can point you to a parts list and instructions.
As for the first picture, it looks like someone replaced a transistor and resistor. Can you put your multimeter into Ohms (resistance) mode and see what you get with one lead on each metal leg on R43? I'm concerned that it looks "black".
Regarding the 6 multiplier lights, if the shoot again and spinner lights work, then the issue is not the entire lamp column in the lamp matrix. More likely your voltage wire (yellow) feeding into the 6 lamp board is either not fully seated in the connector, or is not getting continuity from it's connection. I'd have to check my Whirlwind to see where this yellow wire connects to.