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1993 Fatboy Running Rough

If they were excessively black it could indicate a carb problem but the plugs will show some black around the base ring most of the time. A ride that allows the engine to reach full operating temps and stay there a while will clean them off mostly but the base ring will still show carbon.
 
The plugs were black and sooty, but they were dry. What Iam guessing is that the bike runs rich, or could it possibly be from bad gas?
 
At this point it could be bad fuel, clogged fuel inlet screen, varnish/gum in the needle seat area or CV carb/slide or debris in the float bowl. May want to drain the float bowl in a clean glass and see what comes out. May also want to pull the air cleaner and look in there to see (and smell) for bad gas/varnish. The bike being 15 years or so old has seen enough time for buildup of this kind. A can of Gumout spray and once in a while use of Chemtool, Sea Foam and Stabil (if stored) will suit you well. Good luck on your search and keep us posted as to your results.
 
After doing some research I replaced plugs, wires and ignition coil. The bike seems to be running a little better but there is still the "clinking" sound seems to be coming from the front cylinder. When the bike was running a blue flame was shooting out of the front cylinders exhaust pipe. Also there did not seem there was the same amount of pressure coming out of both pipes, front seemed less pressure, and felt cooler than the rear cylinder exhaust. If it were a carb issue wouldn't it effect both cylinders? Could it be the ignition module? Or something internal in that cylinder? The bike has 43000 miles.
 
Sorry for jumping in here as I've only been on the site a few times and not recently. What bothers me was the tin can sound you got and noise you're still getting. To me I'd take a compression test and see if there's any pressure difference in the front cylinder. Being it's a 93 and not knowing if the lifters have ever been replaced, it's not unheard of to lose a lifter roller which will effect a cylinder balance as it wears the cam lobe. Just a thought, I've seen that many times before.
 
Could also have a lifter going bad, if it will not hold pressure that could cause some noise, especially after it is warmed up.
 
Thanks for all the input so far, Iam determined to get my scoot back up and running. Trying to squeeze all the riding time I can before this Syracuse NY weather takes a turn for the worse.

Checked the compression on each cylinder. Both cylinders are approx. 140psi. Possibe the timing is off on the bike? Ignition Module? Or Carb?

Iam trying to test the ignition module, my manual only tells how to test the module up to 1990, I have a 1993. I am checking the Power supply diode(using the same process as a 1990) connecting the negative lead to module ground black white and the red lead to the postive white wire on the ignition coil, not sure if they are the same, but for a 1990 it states that you should get 800-1300ohms, thats also stating to use th HD multimeter. I am measuring using my fluke and Iam reading .4 to .5 ohms

Would it be possible that if the ignition module is faulty that could cause the knocking sound if the spark plug is not firing when its suppose?
 
I think you need to concentrate on the noise and the actual sound and location. Is it a knock, as in advanced timing or miss fire, is it a tin sound, as in something hitting something????? From there you should be able to pin point more of the area, ignition versus mechanical. You said the front cylinder didn't seem to fire like the rear. Have you swapped the plug wires, front cylinder to rear to see if there was any firing change?
 
So heres where I am, Started the bike last night to try to pin point the sound, tried the screwdriver thing and I could not tell anything. Going to pick up a stethoscope today.

The bike would run decent with the choke on but once the choke was turned off the bike would cut out, if I tried to save it with the throttle it would still die, seems like it was not getting enough fuel. So I took off the carb and in the process of looking it over and giving it a cleaning.

This is the first time I have ever messed with a Carb, so should I use carb cleaner or sea foam to clean, or tear it down and just do a rebuild?
The manifold seal that holds the carb looks good. The thin rubber diaphram piece also look good. Even the screw heads and hardware look good, and I noiticed a Arlen Ness Big Sucker intake on the bike. Iam starting to wonder if this bike has had work done, there was also a washer missing on one of the crankcase breather bolts. The bike was real clean when I purchased it from a HD dealer, also was just recently repainted, it seemed like it was taken care of by the previous owner.

Iam starting to lean more towards the Ignition Module.

Once again thanks for all the input, I appreciate it!
 
So I cleaned the carb and reinstalled, the bike will stay running better and theres better throttle response. But now the carb leaks fuel out of the overflow tube when the bike is not running.

The noise is still in the front cylinder, I listened to each rocker cover and there is definately something going on in the front, sounds kind of like a rattle coming from the inside.
 
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