That port work looks very nice. I always feel bad about assembling such nicely ported engine parts. It's like hiding art work in your closet instead of hanging it on the wall.
Something to consider on balancing that may help in understanding things. Crank weights can counteract the up and down forces of the piston and rod. The weights go in opposite directions. When the piston goes up, the weight is going down and vice versa. What is not corrected by the crank weights is the front and back force created when the crank weights are at the 3 and 6 oclock position. This is one area that balance shafts help improve. You will always have some part of the cycle where the piston/rod and crank weights are in a position that creates vibration. Balancing can help limit that and move it to a different RPM, but not eliminate it. If you ever have the opportunity to see an older Harley idling look at the front wheel. The flywheels on a Harley are massive and the whole bike appears to move forward and back a couple of inches at idle. On some of the newer (and older) bikes the engine is rubber mounted to reduce the vibration felt by the rider. The engine dances all over in the frame. On some of the later bikes the engine uses a balance shaft. These are all ways to reduce the vibration felt by the rider, but it does not eliminate it. BTW...before you guys
flame me, I only used Harley because it is an extreme example that makes things easier to visualize.