Macc- I'm no expert on GL1200's, but it's clear to me that's not just a tick and a fuel pump problem... That's at least two cylinders not firing. You're driving a GL600 engine, with two extra cylinders flailing about. The fuel pump you had was obviously working, but with two dead cylinders, you'll have no power.
Please don't take this with offense- Your approach to the problem is not analytical, and your actions are simply making it worse.
At this point, it's impossible to put it back the way it was... burnt wiring is a nightmare with something as heavily electrical as this, and you cannot 'return' a carb set to prior synchronization with it missing two cylinders, so straightening it out will be no simple task... but First, you need to take a closer look at what is happening, and what it's condition is, before changing things.
If you were me, you'd apply the 'general health check' process of any internal combustion spark engine:
You'll need a a spark plug wrench, flashlight, compression tester, an infrared thermometer, a can of flammable spray-lube of some sort, and a pencil and paper, and a permanent marker.
Mark each plug wire, Remove each spark plug, write the cylinder number on it. look at each one closely. Look for physical damage, broken electrode, insulator shattered, etc. Look in each cylinder, you may not be able to see much, but if you see ANYTHING, make note of it.
Turn kill switch to OFF. Crank the engine over, and note wether anything 'blows out' of the plug holes when you do. that'd include dirt, metal, coolant, oil, or fuel.
If anything blows out, find out what, and why.
If nothing blows out, connect compression tester to each cylinder, open throttle, and crank the engine a half dozen turns. Record the reading of the tester. Disconnect, close throttle, put in a teaspoon of oil, crank engine over a few more turns, reinstall compression tester, lock throttle open, and crank again, and write down the test results. Repeat for each cylinder.
Next, connect spark plug to each wire, but don't install... instead, place them ON the block in such a way that the outer electrode is grounded to the block. Turn kill switch to RUN, crank the engine, and look at each plug. Got a spark? Look at the color... reddish, yellow, white, blue? Write it down (easier to do this after sundown, as they're much easier to see).
Set gap on plugs per spec, install plugs, connect wires, start engine, allow it to warm for about thirty seconds.
Point IR thermometer at the exhaust port tube of each cylinder. Measure temperature, and write it down for each cylinder.
Shut it off, and look at the numbers. The results you get, will tell you which ones aren't firing, and in the process, you'll probably figure out other things that may be clues as to why.
Once you've figured out which cylinder(s) aren't firing, you can remove the vacuum port test screw from a problem cylinder, stick your spray lube tube in there and give it a short shot... if the cylinder starts firing, you know that it's not getting fuel, that means you're in for yanking carbs. If the cylinder DOESN'T, then you've got some sort of valve issue, that would likely have been detected in the compression test process noted above.
Regardless, since you've altered the synchronization, you're gonna need a synchronizer, and best to use a 4-tube sync kit.
My gut feeling (and again, I'm not a long-time GL owner, but have had many motorycles) is that you're gonna hafta pull the carb set, give each carb a really thorough cleaning, a complete rebuild kit, and reassembly and synchronization. I suspect you'll also need to pull the valve covers and inspect the valvetrain, as you likely have problems in there too. Mine has a faint tapping, but nowhere near as hard as yours... my compression is good all around, and the #1 cylinder drops out only at idle, so I'm fairly certain that my low-speed orfice has some crud bouncing around in it. if/when I figure that out, I'll post it in my thread.
