have you checked to see if the keyway on the flywheel is still lined up with the c on cannondale. To do this you pull the cover off on the right hand side, unbolt the flywheel and pull out the lock washer. You should be able to see the groove where the keyway should be. Yes it will throw the timing of the spark off because it is what tells the ecu when to fire the coil.
http://forums.cannondaler.com/viewtopic.php?t=1165
Cannondale Wont Start
This post is from cannondalers.com
I know this might sound silly,but if your engine wont start,check engine very closely.My 2003 cannibal quit on my son and wouldnt start back.He said the battery went dead.Ichecked the battery and sure enough,it wouldnt charge up.I changed batteries and tried it.I was getting spark,fuel,and my flywheel lined up with the C in cannondale,backfired a couple of times,then nothing.I thought my Hex code in computer was corrupted.My good friend Maz checked it for me and told me ECU was fine.I then pulled the valve cover to have a look.My decompression mechanism was busted,a piece of it got between intake cam and valve cover,stopped the cam and sheered the timing pins in the cam.That is why it wouldnt run.Wistech had talked about this on the other forum,listen to him,if your machine has very many hours on it ,check the decompression mechanism for slack in the pin on it,if it comes loose, its NOT GOOD!!!!!!!!!!!!!!!!!!!!!!!!!!
I know this might sound silly,but if your engine wont start,check engine very closely.My 2003 cannibal quit on my son and wouldnt start back.He said the battery went dead.Ichecked the battery and sure enough,it wouldnt charge up.I changed batteries and tried it.I was getting spark,fuel,and my flywheel lined up with the C in cannondale,backfired a couple of times,then nothing.I thought my Hex code in computer was corrupted.My good friend Maz checked it for me and told me ECU was fine.I then pulled the valve cover to have a look.My decompression mechanism was busted,a piece of it got between intake cam and valve cover,stopped the cam and sheered the timing pins in the cam.That is why it wouldnt run.Wistech had talked about this on the other forum,listen to him,if your machine has very many hours on it ,check the decompression mechanism for slack in the pin on it,if it comes loose, its NOT GOOD!!!!!!!!!!!!!!!!!!!!!!!!!!