I would guess maybe a VCO ot IF alignment, rather than an LPF but I'm just guessing. Any thoughts?
No, if you are on frequency, the VCO is fine. The IF is for receive and sometimes used in the SSB circuits, but not CW.
You may indeed have issues in the LPF , though. Could be as simple a as cracked solder, burned relay, or bad component.
look for the common point for all of the affected bands.