Modded BM clone ... when I play the amp with an attenuator and headphones, I'm hearing a ghost note at higher gain settings. ...
The amp is probably fine, the "Ghosting" is simply a normal result of of distorting the power section hard with that attenuator.
On another forum, we had a 10-page thread where someone had a hard time believing this was normal for a vintage-style amp. I can't recall if he had a Soldano or Dumble-style clone, but noted they didn't have the ghosting problem.
But in those cases, the power section distortion was minimized because of preamp gain & master volume, and the lower power output due to master-volume use caused less current-suck from the filter caps. Add to that the much higher filter cap values in those amps, and suddenly the ghosting is much reduced.
What happens to cause ghosting is the burst of high output power causes the power tubes to suck big current from the reservoir and screen filter caps. When current draw increases the hum level at those caps goes up, related to the pulsing DC the rectifier is supplying to try to re-fill the caps. This increased hum is then modulating the desired guitar signal, and the distortion causes sum+difference tones to be created. The "sum tones" get lost in all the other harmonics created by distortion, but the difference-tones become out-of-tune stuff you can hear.
What now?
You kill ghosting at high amp-power-levels by cranking up the filter capacitance for the power tubes. Seeing 220µF per filter stage (4x 220µF caps in series-part parallel) is pretty normal for some high-gain amps that don't want the power section distorting or sagging.
But when you crank up the capacitance, the amp-feel gets stiffer, because power supply sag is greatly reduced. So the amp may seem "stiff" or "brittle" at lower volume.
It's a tradeoff between vintage-feel for clean or lower-volume distortion, vs hearing ghosting when the amp is cranked. FWIW, there's all kinds of ghosting present on classic guitar solos that is only audible when the guitar is isolated from the track. But guys playing with attenuators and outside the context of a band/song-track start noticing these things that always happened, and didn't matter until they put stuff under a microscope.