Just to get things started...I am on the road tomorrow, so this will probably be my only entry for a while. So I hope others jump in....
Is the noise coming from the upper part of the crank or the lower?
If the upper, you are just going to have to remove the top plastic cover and see if anything is loose or rubbing external from the crankcase. i am sure you have taken a long screwdriver against various areas of a motor and the handle up to your ear, like a stethoscope. (Or use a stethoscope if you have one)
If the sound seems to be coming from under the crank pulley in the crankcase, the next step is to remove the timing chain cover to check the timing chain. One of the chain guides may have broken or come loose. Parts 11 or 12
http://www.boats.net/parts/search/H...d Later/BF135AK0 LA/CAMSHAFT VALVE/parts.html
It would help for you to check the codes to see what is causing your check engine light to come on..Find the red 4 pin connector on the side of the engine. Using a paperclip short out the light green/white and the blue leads. Careful not to cross it over to one of the other leads.
Turn the key switch to on and watch the check engine light. Count the long and short blinks and let us know what you find.
Check the codes first....that may help you locate the problem quicker.
Lastly, if you are reving the motor up above 2000 - 3000 rpms when the engine is in neutral, the engine will shake and bounce. It does not want you to do that when it is not in gear. If you must do a quick rev up, put it in gear. You should not rev it high without being in the water. But, try what you were doing before but do it in gear, just to eliminate the shake as a problem. Then again, there may be a problem. That is the only way to tell.
Good luck.
Mike