You know I've always had a noisy train and it only bothers me at low speeds. At least that's when I notice it most, but once on the road cranking out say 3500-4000 there's none of that nonsense to be heard. When I crank up cold I go 'OMG.. She's gonna blow!' Once warm and going about business it sounds like a Commando and I don't worry.
The only thing noisier than a Commando I've ever heard up to is an old panhead. You could have an issue or it could just be anxiety..... I get it every time I rebuild something because the pitch and vibration levels change making me suspicious. It takes a while for my confidence to return.