The phono stage on the C11 has 3 tubes in it. V1-V2-V3 for 3 sections of 12ax7 gain. Check them for mismatched sections and poor emissions and gm, clean pins on tubes, and retighten tube socket leaves. V3 especially as each 1/2 runs a channel, you'll see it in the scat. Are you hitting the same spot on the the Volume control in AUX as in Phono?? If you are using more volume in Phono than Aux, try that volume setting in Aux, tuner, etc. If it DOES NOT scratch or crackle then, the volume control is NOT at fault. If it does, the Volume control is at fault.
As I thought, Aux is injected into the circuit past the phono circuit, directly into the Balance control, then the Loudness and Volume and then V4 which is the 2nd stage. Phono is the 1st stage. So unless the Volume pot is suspect which I don't think it is, unless the settings for Phono and Aux are totally different, the phono stage is the prime suspect. Loose tube socket leaves, worn tubes, or coupling caps. As you stated that in AUX you had no problems with Loudness, or Volume (try the Balance pot also and post results), just phono, and both phono and Aux end up both going thru Balance, Loudness, and Volume, the the problem is most likely in the phono section.