Be sure it's not a slightly noisy clutch - pull the lever in. Does the noise disappear?
Leaking exhaust flanges are also more common at startup than later. On Carlos' project, even with a standard manifold I put in 2 front gaskets to get a good seal...
You might also want to check the valve clearances if they haven't been done yet.
They're usually pretty solid engines.
Might want to do an oil change (10W40 synthetic), how clean is the oil?
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