I would try using the IF Shift function in the KD8CEC software to see if that helps. There could be an alignment issue between the 45 MHz roofing filter and the second IF vfo. The IF Shift changes the second IF vfo frequency a small amount in either direction.
The other thing that I would try is to remove the AGC function with Q1 by removing the gate signal. Q1 could be drawing down the input to the audio amp too much. I do not see a way to adjust that level.
Just suggestions for you to try.