I emailed arrowheadep the other day about their cranks not having the 3rd timing marks, this is the response I received:
Good Morning,

Our production / engineering team has responded with the following :

" I dug far back in our records and it looks like we have never put timing marks on this crank. In addition, we don’t have any specific instructions for timing. The information I have been able to find suggests that you just go by the timing marks on the OE crank. I know that isn’t a great answer, but it’s the only option I see at this time. "
 Not sure if this link will help or not.

http://www.suzukiquadracerhq.com/lt250/alignment-of-crank-counter-gears/

 Sorry we don’t  have better info!

Thanks, Brandon