yea the crank sensor is diffrent and I think the ECM's read the readings diffrent.
so you have to the same mod I did and put in a crank sensor and sprocket from a 01
problem is you can't get that sprocket off with out the front cam chain guide out the way
so you have to remove the head or break the bottom of the guild off
then set the gap to the 01 pick up to around .012"
Mine works great with an 06 engine in it now
I did put the 01 head back on it to save $$