CBR600 "Missing" Below 4K RPM - HELP!!

I have a very pristine 1993 CBR600 that has always run perfectly.  Not one problem!!  Very clean and all maintenance done before due.  It does have 40K miles on it but it looks like it just rolled off the showroom floor.  Extremely clean.  Recently, I noted that it starting "missing" while idling and seemed to be "cutting out" and running rough on the throttle below 4K RPM's.  I replaced the spark plugs but that did not cure the problem.  I drained the fuel tank and replaced with fresh gas.....no change.  The bike does not sit.  I use it to commute to work.  The engine is still poppping and runs rough.  It's like it "stumbles" slightly when on the throttle.  Why at low rpm's only?  Above 4K RPM's it smoothes out again.  Is the wiring harness the next thing to replace?  It's probably the original harness.  Possible electrical problem (rectifier or ....?)  Don't want to go hog wild here without some kind of a road map to guide me through the most obvious.  That's why I'm checking with you folks in the forum to see if anyone has had a similar experience and found the solution.  Appreciate all the help.  Love the bike and because it looks and *has* run like its practically new, don't want to give this one away.  Thanks for taking the time to respond.
 

I doubt it's the harness. It's a 1993, so I doubt it has fuel injection (pardon my lack of knowledge with older bikes). It has a carburetor, yes? That's what I would check first. Had an older car with a carb, and was always sputtering at lower RPM's, and it turned out some of the vacuum lines were corroded and the carb needed to be rebuilt.

But I'm just taking a shot in the dark here. I'm not familiar with older bikes, but rather with older cars.

Check your battery voltage at 3500 and then at 6000rpm, maybe your thought on the charging system is on target, it doesn't cost anything to check that out.
 
+1 on the vacuum lines, my old vette is really a vacuum nightmare, pop up lights, wiper door all run on vacuum, when there is a problem with the vacuum system, the car won't even idle. Look for cracks in vacuum lines.

Check this link.  I really suspect it's the E-10 gas issue.  Your primary jets are probably clogged and need to be cleaned with either some sort of fuel treatment or possibly manually.  I've had the exact same problem.  Because the primary jets are smaller, they are more prone to clogging, which explains why your performance above 4G is unaffected.

Good luck!

http://www.cbrforum.com/m_397526/tm.htm

JRM

+1 on the carb/jet issue. I think the people near me call them slow speed jets, but they all say they can get clogged easily. The 10% ethanol blend has been around for many years, so i'm not sure that would be the cause, but it does seem like it needs some cleaning.

I think mk hit it perfectly. It sounds like a primary jets.

my brother-in-law had same issue w/ his 93 ninja,had his carbs rebuilt (new needle and jets). THE BIKE RUNS CHERRY NOW.