Op Amp Clipping High when Signal Goes Low
Your 4558D JRC is a sad copy of the sad old 741.  

It doesn't have much operating space when powered at 9V.  

The inputs and outputs must all stay about 2V from the powersupply rails.  That leaves you with about 4V of input range and 4V of output range centered around 4.5V.  

Call it 2.5V to 6.5V as valid input and output ranges.  

Exceeding either of those limits will cause the op amp to misbehave.  How it will misbehave isn't really defined.

You are also using a fairly high gain, so you will easily exceed the available gain bandwidth with just audio signals - leading to more distortion.


Use lower gain (maybe a couple of AC coupled stages with lower gain instead of one high gain stage.)
Make sure your input signal stays within the allowed boundaries.
Make sure your output signal will stay within the allowed boundaries.
Clip with diodes rather than depending on the opamp to clip when you overdrive it.