you mean it has .005" run out.. right??
to check phase you need to measure in between where each cylinder is at tdc to make sure it is 120 degrees. If you suspect a phase problem you can check it quickly by removing all 3 plugs, then make a mark on the engine case right above the clutch at 12 o clcock. Then using a long handle screwdriver insert till it touch piston, rotate the engine via clutch till screwdriver is at tdc, mark the clutch in line with your mark on case. Repeat this for all 3 cylinders. when your done take a cloth measuring tape and measure around the clutch to your marks, should all 3 be the same , if not the crank is twisted or out of phase.