The screws in the boots are removed when you are balancing your carbs - they're normal.
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The screws in the boots are removed when you are balancing your carbs - they're normal.
Where did it go?
To test the coils put one probe of the multitester on each of the terminals on the primary side of the coil. You should get 3-5 ohms. Check the secondary windings by placing one probe into each of the plug wires coming from one coil. Those would be 2 & 3 from one coil and 1 & 4 for the other. You should get 30-50,000 ohms for stock coils and 15-20,000 for aftermarket.
Dyna S already installed? BONUS!
Yes, on my GS550 left feeds 1 and 4 and right feeds 2 and 3. More importantly, with a Dyna S the 1 and 4 coil should be grounded with the WHITE wire and the 2/3 coil the BLACK wire (from the 3-wire Dyna harness). The RED 12V feed for the Dyna can come off of either coil (the orange/white wire) or any other constant 12V source, it doesn't matter.
Don't charge the battery with more than 2A current. Use your voltmeter to ensure your orange/white coil wires are getting ~12V with the ignition on. If they're not the coil relay mod may help, if they already are don't bother. Instead of the coil relay mod, you could have a field day cleaning connectors, particularly around the ignition switch. That's usually where the voltage loss is.
Splicing the Dyna wires in is pretty normal. With the points gone the other end of the wire goes to nothing.
A strong spark should be "fat" and blue. Weak spark would be thin and probably orange. I know that "fat" and "thin" are a bit subjective... Take your plugs out (are they wet w/fuel?), hook the wires back up, and lay the threads of the plugs against the head. Don't lay them right over top of the spark plug holes, where they might ignite something coming out. Then crank it over and see what you get. You were running on two cylinders so you would probably have at least two strong sparks.
Try putting a few drops of fuel in each cylinder before you put the plugs back in. See if that gets it a bit more active.
I know you said you have a 4-into-1. Is your bike still running a stock air box or do you have pods? Cleaning carbs - the right way - is the remedy for 95% of "GS has been sitting, now won't start" issues. The guy who looked at your bike said it had weak spark on two plugs but not sure I'd take him at his word on that. He didn't even notice that the plug wires were not in their proper places...
I'll check the jets to see if they are still to spec. Now to figure out what the specs for the jets are..??