If you have a manual then you are half way there.
I have a hard copy Clymer and a soft copy of some unknown manual off the net.
They disagree about valve operation and position when setting the timing
Just goes to show you still need some nouse when playing with these things. Unfortunately with electronic ignition modules there is no way of following the circuit without a diagram as the circuit gets lost in the module. Having had my 900r apart several times now, I am familiar with all the timing marks.
Without looking at the bike and plying with the leads and timing, unless you had/have the same bike, you are just giving estimations.
Good luck and work logically, random adjustments of shit does not work
http://www.gpz600r.com/electrics.htmlmay be of some help