The resistors would cause a crackling so if it’s an overtone or distortion, it’s probably not a bad resistor. Interesting that the NOS rectifier tube(s) you have are that close to a new one. I have a number of NOS 5Y3s, RCA and Sylvania mostly, and they all measure around 40 volts (give or take) lower than a new JJ or Sovtek.
If it sounds like a sub-harmonic (unnatural harmonic like a ghost tone over the note), it could be a filter cap issue, it’s unlikely with new caps, but it’s a common fix for old amps with that issue to replace the coupling caps. The OT is probably ok, but the location might be an issue if there is phantom coupling with another component. Moving it around a little bit would prove it. Also, keeping the grid resistor as close to the socket as possible and shorting wires to the grid helps sometimes. I’ve never seen these issues in a Two Stroke before but everyone’s build is a little different.