The tremolo circuit is a ring/balanced modulator design centered around the four diode ring CR100-CR103. The audio signal is sent into the diode ring where it is modulated by the low frequency signal from the oscillator circuit.
The modulation driver Q113 sends a two phase signal to the diode ring. The resistor 1% values are there to insure that the two out of phase oscillator signals are as even as possible so that the diode ring will work evenly.
I'm not sure what is causing the thumping as you have checked everything that I can think of. Have you tested the four ring diodes? If you want to try finding 4 matched diodes and install them to see if that helps.
It may help to isolate the trem oscillator power lines from the rest of the power supply.