Possibly the transistors, especially the one closest to the 4.7k resistor on Sam’s stripboard layout. If you put 10R resistors in series on your power rails, check those too.
Possibly. This kind of filter sometimes benefits from attenuating the input.
[Especially if it’s the LMNC VCO, or any 3340 based VCO that doesn’t rescale the outputs; then the different waveforms have different amplitudes, and the square wave is the biggest one.]
Yes adding an attenuator pot on the input works well and also allows you to be able to adjust the “drive” in some way the power of the resonance on the output rendering