When you re-assemble the shafts, the flanges need to be at 90° to each other. If you don't it will cause harmonics, i.e., "bad" vibration in the shafts themselves.
You mean the engine WASN'T dyno tuned and the shop HAS a dyno. That's where you run it in, setting the valves, the timing, the carb jetting, carb float level, checking for leaks, etc.
Was that an "extra" that you said no to? By all means, put the thing on the dyno. That's your chance to fix what needs to be and build confidence that it is set up correctly and ready to run.
That's the most scientific you can be with the engine.