Like any hi-perf race/freestyle motor...Use a dial indicator in the sparkplug hole for a degree height from the piston, then put on a pointer and scribe mark on the coupler drive and run engine to check with a timing light (unless you have a new digital MSD-TL)
What ignition are you running? I can look at my timing charts (what stroke your running/stock is 74mm) to give you a piston height, lets say if you want to check timing at 24 degrees. A stock Kaw 750 is 743cc's (80mm X 74mm ) 1st over is 80.5mm bore would be a 753cc.
750 small pin running first overbore wiseco 752cc, and 650 electronics with the steel hub Jetnetics, stock stroke. This issue with advancing 5 degrees due to the strong magnets kind of baffled me, I just want to get really close the first time. The exhaust port has been raised and widened , transfers are stock. I was advised to run no base gasket and just 1211, and a copper head gasket to help lower port timing. Also the sleeve extensions were cut at the center boost port. Here are the measurements I took earlier this year.
Ok, exhaust from deck, 40.5mm
bottom of exhaust, 77mm
exhaust width 57mm
side transfer ports, 76mm to bottom, 60mm to top
rear transfer ports, 76mm to bottom, 61mm to top