A crankshaft is typically balanced without the piston or rod on it. From 1/2 the length of the rod downward to the crankshaft is considered rotating mass while everything upward from the middle of the rod is considered reciprocating mass. This is the simple part. Here's a you tube video of a crankshaft being balanced.
https://www.youtube.com/watch?v=LvgVI2PTKzI
It is a multi-cylinder crankshaft while you will be working with a single cylinder unit.
Piston manufacturers try to make even their "BIG BORE" pistons weigh the same as the stock piston, but a large variation in weight is OK because it is the reciprocating part of the equation which does not have as much effect on balance as the rotating part of the mass.
Here's a good article that explains the physics of crankshaft balance
How To Balance An Engine - Engine-Balancing Basics - Car Craft Magazine
The bronze bushing is not important. As a matter of fact, I worked on an old Honda XR that had a seized wrist pin. After extracting the pin, the small end of the rod was damage beyond use. Neither a rod or crankshaft was available. I sent the crank to a machine shop along with a new piston pin. The machinist bored the top of the rod, pressed in a bushing, bored and polished the bushing to fit the pin thus saving the rod and the engine.