Ok , i'm about to go the other way, putting a 03 ecu into the 01, just ordered the trigger wheel, are the 03 keyed with a blank spline ??
As mentioned in the busa section lately you can get a real good indication if your cam timing is close by looking at the end of the cams, besides the .1 on the exhaust cam sprocket there is a = in the centre of the camshaft, that will be lined up with the top of the head facing forward (unless its a inlet on exhaust)
the inlet cam on inlet side will have a - facing to the rear and up a couple of degrees up from level with the head, it these are right even if its not dialed in 100% it still should run.
maybe double check tdc to be sure your crank index is correct and your not getting a false reading through the sight hole