You absolutely can balance a single cylinder engine.
The problem is that you have less weight to work with and can really only balance the rotating assembly (with flywheel) to a specific rpm.
From the factory, most of our industrial engines are static balanced to 3600 where they were designed to spend much of their life. At 3600 rpm, the balance doesn't have to be very precise, but at 10,000 rpm, that balance had better be a lot closer than where it was from the factory if you want that engine to live. Big surprise that we have to loctite sidecover bolts on a clone turning 7000 rpm with stock factory balanced parts.
Now, throw in different bore sizes, different piston and ring packages, different connecting rods, and then throw a light weight billet aluminum flywheel on it, and you'll see that the factory "balance" is a long way from perfect with your new rotating assembly.
We spent a LOT of time testing a balanced flathead years ago through the clutch alone. Was it worth it? Not really. But then again, the engine was $600 as raced. Take a small block open that's turning gazillion rpm and costs upwards of $2500, and I think you'll want to at least consider having it professionally balanced. The benefits are real -- the return on investment may vary for your application and budget.
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Thanks and God bless,
Brian Carlson
Carlson Racing Engines
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34 years of service to the karting industry ~ 1Cor 9:24
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