Not so long ago I had an "issue" after a rebuild when the bike would only run on one cylinder, on investigation I found a rag still blocking the inlet port, whoops!
Measuring piston height to guestimate firing angle is not as accurate as using a degree wheel zeroed at TDC using a fixed stop to calibrate. Still it should be close enough to make it run. Are you sure the correct points are firing the correct plugs when the correct cylinder is on comp.?