Method
A Bonzai plugin is not a set of filters tuned to sound like an instrument. It is the instrument's circuit.
From the schematic
We start from the service documentation: the factory's own drawings and parts lists. Every resistor, capacitor, transistor, diode and op-amp is entered as it is drawn, with its value and its part type.
Solved together
The whole circuit is then solved numerically at audio rate, all parts at once. Stages load each other as they do on the board, so driving one harder changes what the next one does.
Checked
Each model is compared with a circuit simulator running the same circuit with full device models. Where the original's maker published adjustment procedures, we run them on the model in place of tuning by ear.
Where the drawing ends
Some parts were never documented: a sealed gain cell, a custom chip. Where we had to reconstruct one from its published behaviour, the instrument's page says so.
Light enough to use
An instrument is not finished until it runs under a tenth of one processor core with every voice sounding.