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twin cam problems?

I put a twin cam in my 1990 fxrs. used an 04 sportster wiring harness, o4 flt screamin eagle ignition module , custom chrome #605050 coil. The motor is a 2000 screamin eagle with 45 hrs mikuni. Bike will fire run for a second and die, Will not fire again until I quit cranking the starter, then will do the same. Tssm has been bypassed. Seems to be firing on rear cylinder even though front cylinder has spark.
 
Seems to be firing on rear cylinder even though front cylinder has spark.

Joe, I don't understand what the above statement means..

If you were to remove both plugs, hook up both coil leads to the plugs, ground the body of both plugs to engine and crank engine.. do you see repeated firing on each plug? And even for the fraction of a second after you release the cranking button and the engine is spinning down to 0 rpm, do you see a couple of firings? How is the ignition module triggered. Is it self contained with its own trigger circuit (photo, hall effect, reluctance etc)?
 
I have both cylinders firing now had a short in the plug wire. but still have the problem of it running for a second then dies wont fire again until i release the starter button and push it again. it starts immediatly barely a full rotation of the crank. the module is self contained
 
So it's only running when you first crank it off basicaly right? If this is the case I've had this happen on old chevys before. Check to see if you have power to the ignition module only when the key is on and not cranking the bike. Sounds like the power is flowing through the selenoid wiring when cranking but now steady power to the coil and or the ignition module. Get a wiring schematic and make shure you got power to the module when the key is on. Good luck.:s
 
I put a twin cam in my 1990 fxrs. used an 04 sportster wiring harness, o4 flt screamin eagle ignition module , custom chrome #605050 coil. The motor is a 2000 screamin eagle with 45 hrs mikuni. Bike will fire run for a second and die, Will not fire again until I quit cranking the starter, then will do the same. Tssm has been bypassed. Seems to be firing on rear cylinder even though front cylinder has spark.

Change the ignition system, something wrong in there, probably the module
 
I dont get it. What year is your Twin Cam motor? What ignition system are you using? I have a Twin Cam motor in my FXR and as you know ignition is triggered from the crankshaft sensor. I am using a Thunderheart Stand Alone single fire ignition. Works fine.
 
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