We'll just have to see what it does in crank mode later on. You could pull the wire on the starter solenoid to keep it from engaging; then with the key in START position you'll be able to see if the bypass wire gives the 12 or so volts on the load side of the resistor.
You don't want to do that, because you want to measure this under "real" conditions. You want to measure with the system loaded, just as it would be starting
OK, so I started from square one. Pulled the dark blue line that didn't have voltage and pulled all plugs off the coil side and turned the key on. Got about 12 volts on both sides of the resistor. So then I connected up the brown wire and it stayed at 12 volts on both sides. I then added the wire that goes to the coil and it dropped down to 4.6 volts on the coil side and 11.4 on the other. I then removed the wire that went from the + post on the coil to the electric choke and the voltage went up to about 5.3. I am not sure if that is telling me everything is OK? My son just went to bed, so I can't crank it over to see if it starts up right away or struggles like it has in the past?
What you described shows it's wired OK, but you ARE in fact getting a lot of drop through the harness. 11.4 is nearly a ONE volt drop from the battery. Too much. You need to chase this down. See if you can get your meter on the back of the ignition switch, and/ or on the interior side of the bulkhead where the blue wire comes through.
You have wiring diagrams?
It is important to measure with the ignition all hooked up, because this 'loads' that circuit. If you unhook all loads, you remove the voltage drop, and it will measure "same as battery."
You want to check your ignition bypass under "real" conditions with the starter cranking.
Remove the coil wire, and hook it to ground
"Rig" your meter so you can see it when operating the key, one probe clipped to battery positive, the other clipped to the coil side of the ballast. Make sure, as I mentioned, that the ignition is all hooked up.
Now crank the engine using the key, and see what the meter reads. You are measuring "voltage drop" from the battery--through fuse link, through bulkhead connector, through ammeter circuit, through ignition switch connector, through the switch and back out the connector, BACK through the bulkhead connector (on the brown wire) and to the coil.
You are looking for a low reading, the lower the better, more than 1/2 volt is too much and shows a problem in the above path somewhere.
Finally, a rough check of your battery starter condition can be made by measuring right at the battery while cranking. Absolute "low" end is 10.5V. If the battery reads that low, either the battery is discharged or in poor shape, or the starter is drawing way too much current.