Why did you replace the battery etc? Did this start before or after that? Could be a number of things. When does it happen? All the time or upon acceleration etc? I would start with a new set of plugs and go from there.
Please post a comment if you have more information to provide or if you get an answer etc.
SOURCE: When bike gets worm it runs like ****
Since you have thrown the entire ignition system at it, let's think about fuel. If you were running out of gas it would act as you described. I would start by removing the float bowl. Be careful not to spill any gas because we want to look at the level. It should be over half full. Check the float movement. You should be able to push it up without resistance. Looking from the bottom remove the phillips screw that retains the float axle and the float and needle valve should fall out. If the needle valve has three sides or if the rubber tip is worn, replace it. The 3 sided valves have a tendancy to stick closed and all dealer stock should be the 4 sided version by now. After you re-install the float, leave the bowl off and follow the small vacuum hose from the petcock to the carb. Pull it off at the carb end. Look to make sure it isn't damaged. **** lightly (sorry) or use a vacuum pump on the hose. With the petcock on and gas in the tank, a healthy stream of fuel should pour from the needle valve. If not, the petcock diapragm is shot. If none of this helps, take it for a ride and when it acts up, crack the fuel cap loose and if it takes off the vent in the cap is malfunctioning.
SOURCE: my 2006 dyna street bob efi back fires
that is usually caused by a too rich main jet
dumping too much fuel and it is igniting it in the pipe
SOURCE: not charging the battery as i ride 2002 dyna fxd
heck all connections especially the one thru the motor to the regulator-check battery to make sure levels are good and have it load tested
SOURCE: how to change oil in 2003 HD FXD Dyna Super Glide
remove the drain plug from the oil pan, you will need either a 3/4" box wrench or a 5/8" box wrench and the drain plug will be facing forward on the the oil pan. It is easiest to remove this drain plug from under the right side of the bike. put drain plug back in after about 10 m,inutes of drain time and tighten to 18 ft. lbs. Dont forget to change the oil filter as well.
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