I recommend a two-step process. First remove both flywheels: Construct a basic device out of scrap 2 X 4 piece about two feet above the flywheel laying flat on the ground. Through the center of the hub, you will run a cable or rope down from the 2 X 4 support above. If carefully positioned in the center of the hub, the heavier side will lean down. Apply stick on wheel weights to the opposite side until the suspended flywheel is level. The most difficult part is constructing a plug in the center of the flywheel hub to precisely center the lifting cable. CUJET had a cone which we drilled a hole through the center and threated the cable through. I think Home Depot sells wooded cones in the wood finishing section, if not, make something out of scrap metal.
Step one will get you very close assuming the internal balance weights are correct. Now for step two. Install your flywheels back on the engine and see how they run. Perhaps you are done. If not, do you own an iPhone? Then down load from the apple store this $4.99 application.
https://itunes.apple.com/us/app/vibration/id301097580This program uses the iPhone internal accelerometer which runs at 100 Hz. You can measure and graph vibration in the X, Y, & Z planes. It does a really good job on low frequency vibration and only costs $5. You are only interested in the X & Y planes on a single cylinder. Check the graph, how much vertical vibration / acceleration do you have? Remember there is a power pulse on the piston. Try adding weight at a point on the flywheel. Did the vibration get worst or better? Repeat until you fine tune the rotation. You will never get it perfect, but you can measure your progress with each trial run and engine start. Keep a log book, divide you flywheels into at least six (6) 60 degree slices, twelve would be better, masking tape works well, and number them, 0, 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360. This is a time consuming process to fine tune your flywheels. You might get satisfactory results after step one, but if you need to go to step two, you can apply a lot of lip stick to a pig as I have done.