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more good things to check from Goose. Except, the Vulcans only have one carb, so don't spend too much time looking for the second carb 
The petcock could be a valid issue perhaps, - but I think your symptoms don't fit - it would act like it were running out of fuel.
Check the terminals but don't forget the minus is going to the bikes engine or frame and this connection counts just as much as the ground cable on the terminal. There can be rust underneath.
In fifth gear the bike should be past the point of vibration and it starts right up so I do not support this hypothesis.
A vacuum petcock can either be unable pulling a small rubber or the rubber leaks fuel trough the vacuum line to feed one cylinder, past or only just to one carburetor. Check the hose for being rightly connected and not being kinked. Next do check for fuel in this line. Check the fuel filter and the gas that comes out from the entrance side. All of a sudden the tank can produce residue and skin that looks like clear coat, from long storage periods.
The vacuum petcock can be combined with a manual petcock that has a a Pri (prime) position. This provides the bypass. Manually automatic petcocks can be bypassed for diagnosing by a (I used 8 millimeter outside diameter on a Honda) T. This can be brass or fuel resistant nylon from the car parts shop. When bypassing manually is necessary then plug the vacuum hose. Duh.
Because it is so easy you should check the alternator for charging capabilities. Determine the Battery its Voltage to be 12,8 Volt or close. Any higher is not long maintained. Then start the engine and read the Voltage on any idle throttle given. This number must be between 13 and 15 Volts. Right in between is ideal. It should not go down far or higher up with high revs.
The coils can short the ignition and who knows cause unburned fuel. They often start doing so when the coils are hot. A defective coil can be recognized by burn spots on the outside and testing for continuity. Do not forget to check the spark plug cables on both sides, the coil side and the cap side. My 1500 had one loose cable, they are simply turned and pushed with their core onto a threaded object, like a screw.
Testing the coil explained on YouTube.
https://www.youtube.com/results?search_query=testing+ignition+coil+with+multimeter+
Again I do not think this to be caused by the carburetor because wrong mixture would probably seize the engine longer and/or cause problems when the engine is cold. What you could do is check the carb boots seams by spraying small amounts (!) of liquid lighter-gas (airosol held upside down) or other burnable gaseous liquid (deodorant for example) right there. Let the engine run on slightly higher refs with the adjustment knob. When boots leak the idle goes up noticeably. Please be careful not to let the spark plugs ignite those small amounts of spray and better not have the engine running inside the garage ever.
Cough is a funny word -can mean different things to different people. I deal with this for my job with customers every day - getting them to describe the problem is half the battle. Something you said in your last post makes me think it sounds like its only running bad under load, i.e. lugging the engine (lower rpm range). You mentioned only in 5th gear - sometimes in a headwind. I'm not a great bike mechanic, but if it were a ford truck, I'd wager it was a bad coil. An ignition misfire is more prevalent in high gear, under load, lower rpm, slight uphill or slight acceleration. If you downshift or increase revs it is better. A bad electrical connection, like Troll said, will cause the ignition to cut out momentarily. I don't have enough experience with this ignition system to say if that would also be more prevalent in high gear or not- but that's the easiest thing to check, to start with. Make sure you check connections not only on the battery - but also ground to frame - if the frame ground is loose, it's the same as having the battery connection loose. Might as well check wiring and grounds on your coils and ignition as well, while you're at it.
Is the problem you describe as a "cough" more like cutting out of the engine? (i.e. instantly turning the key off/on on or many times), or is it a "period" of running "rough" like an engine miss? Any more description you might help the experts figure it out.
Did this problem just start with a certain tank of gas?? Bad gas can cause a problem, although not as likely to fit your description.
I'm wondering too, if it's a coil starting to fail.
Anxious to hear back on what you find.
I don't notice this in any other gear except 5th. I rode about 100 miles this past weekend only coughed when I felt a strong headwind running about 65mph in 5th gear. At times it feels like a power loss, like its going to start coughing, and I twist the throttle alittle more and seems to push through the strain. I will pull the plugs tonight to see what condition they are in and report back.
I too am not a mechanic but am dangerous in trying to figure things out that is why I have GB and Troll on my speed dial for help.....
But one would think if it was fuel related it would happen in any gear if you run along in that gear long enough.Some lads were having issues with the fuel venting of the gas caps, most of course were when they had been riding in top gear and long enough for the tank to want to vent. But if you were for some reason on a road that did not allow you to get to top gear and forced you to ride along say in third for the same distance then the tank should be wanting to vent...correct.....
So Oldschool now goes out and checks his battery connections, they are nice and clean plus tight. If that is ok and squared then he goes for a ride, after a bit of a run he hits the kill switch and coast to a stop and removes the plugs and checks for the correct colour, and we move forward from here.
Ratman, but isn't there some sort of pump that's part of the fuel petcock on these bikes? That might be what he's referring to not an actual fuel pump per se. Still anything like that is going to be not related to a gear or a speed you're going but to fuel flow. And again I'm not a mechanic but since he says it's coughing and spitting, it makes me think it's carburetion not electrical--just a shot in the dark.
OK correction: it's a vacuum controlled petcock – I knew there was something different about it – but could this be related to the problem? Here's a link from an earlier discussion about the petcock: http://www.vulcandrifterriders.com/forum/index.php?topic=20936.0
Make sure the battery connections are clean and tight. My W-650 had a similar issue when I first bought it. Riding along, minding my own business, and it would almost seem like it hopped out of gear for an instant....only happened in 5th. Turned out it was a slightly loose connection at the negative battery post. Fixed that, and it hasn't happened in years. NO fuel pump on an 800. Gravity feed to a carb. If the pipes are black, it usually means that you are running rich...but no lead fuels with alcohol may skew that observation. Best place to look for a mixture problem is by looking at the plugs. White, too lean, tan just right, black, too rich.
ok unless I am really off the mark here and we have enough experts that will weigh in with a remedy so, if the bike starts and is running properly in all gears but 5th , I will say it is not the battery, not sure how the kickstand switch would be involved only in 5th gear, I know that the Kaw rep and all the mechanics I talked to said not to use irodium plugs in the 800 engine.
There is no fuel pump on a 800 that I know of. I'll bet it is the carb and it just needs to fine tuned.
I'm not a mechanic so I'm kind of going out on a limb here – can you replicate the problem without going 65 miles an hour in 5th gear? In other words is it when it hits a certain point in the RPM range the problem occurs, so that you can better diagnose it maybe in your driveway in neutral or on a side street in second gear? I'm just trying to help you get a handle on what's going on with your engine, since diagnosis is what's needed and doing that on a freeway ain't very safe. Good luck, ride safe, and let us know what you learn.
I ride a 02 800 drifter. I Grampsized the bike when I bought it used. Runs great except sometimes when I am riding in 5th gear at 65mph, the bike sputters and coughs. Once the engine died but started back out after I pulled the clutch in then back out. I changed the plugs. Old plugs only had 3k miles, looked ok. I put Roadburner dual exhaust on it. I noticed the baffles are black were the exhaust exits the pipes. Might be running rich. Anyway, I have read on forums it could be the battery, it could be the kickstand switch, fuel tank venting etc, etc. One guy changed battery, fixed the problem. One guy ran irodium plugs, fixed his problem. I want to know if Grampsizing has anything to do with it. I also heard maybe I need a new fuel pump. To many maybes. Has anyone on this forum had this issue and if so, what was the fix.
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