Let me see if I can help here. you don't sound stupid. Took me about 3-4 months of asking questions before the basics of schematics sunk in - then it sort of clicked (and the only knowledge/experience I had was an O level* in physics 35 years ago...*UK thing)
First, if you are going to stick this machine, and therefore will acquire others (yes, you will) its worth getting the actual schematic and reading these:
http://www.pinrepair.com/em/ (Clays, and my favorite)
OK, on to yours - see below.
First the two vertical lines in pink is the circuit coming from your transformer that drives the various solenoids, relays, etc (just not the lamps, thats a lower voltage circuit, usually on the other side of the schematic)
Look at my "1" - that's the ball release solenoid (kicks it out). It pulls in when the its "connected" to the 2 pink wires. Well one is already, the right hand side (see green circle), but the left hand side has to go through a couple of switches before it hits the other side (brown circle):
a. first switch 4B on the score motor has to closed ("yellow 2"), its normally open, so as the score motor turns it will close it at some point - you will need to read Clay's site for details
b. a switch on the Outhole Relay (which will be on the base of your cabinet) has to be closed ("yellow 3"). this switch has a yellow white and a Grey wire if my eyes dont deceive me (and if this schematic's applies to yours!)
So, what causes the Outhole relay to close? The outhole relay coil must get pulled in - thats marked with a blue arrow. For that to pull in:
a. There is a normally closed switch on the "Top Eject" relay ("blue A)
b. There is a switch on the bonus unit that has to be closed when they unit is as zero ("blue B")
c. There is a switch on the score motor, Index D, that has to be closed ("blue C")
Here's how I would approach it. Given you suspect your bonus unit, physically look at the switches on it. there should be one with 3 connections (a make/break switch) the colors of the wires to that switch are on the schematic. Make/break means a switch with three "blades" with the middle one either making a circuit with the top or bottom one. (See Clay's guide again!)
When the unit counts back the bonus to 0, the blades with "W-R" wire and "B" wire (see schematic for legend on colors!) have to be closed. When the bonus is being accumulated (as you play) the wheel moves so those two blades open, but the W-R one now connects to the blade with the "something" colored wire (cannot read it - see large blue circle).
Check that make/break is correct. If it is, I'd check the all the switches I have marked (1-3, A-C). You'll figure it out - in the end its just finding out how to get voltage to both sides of something - in this case a relay then gets voltage to a solenoid.
I'll stop there - its a lot to take in, I hope it made (or will in time) make some sense