That is a common problem. You want 1/8” clearance between the yoke and the snap ring in front of the thrust bearing. You can shorten the splined yoke. I would recommend not shortening to the point that the spline length is less than one shaft diameter. That means that you want the actual spline engagement to have at least 1-3/8” engagement.
Before you cut anything, may I ask, what is the cause for the need to shorten the drive line? Did you change drivelines, change or move your engine, reset your pump, add a Jetaway, etc.? If the driveline is too long, flex in the boat will allow the pump shaft to push against the crank, killing the engine thrust bearing.
Actual cutting of the yoke can be done by various means based on what you have available to you. I have machined them on both a mill and a lathe. I have also cut them in a chop saw, with a die grinder cut-off wheel, and even with a hack-saw. The material really isn’t that hard. Ideally, you would like to make a nice straight cut, but the runout of the cut on the face is not critical at all. The face of the yoke does (should) not contact anything. All you want is to maintain clearance to prevent it from pushing against the crank shaft. Don’t cut it too short or the splines could fail.
Cheers,
Joe
