>>So simply putting a transformer in the signal path might cause problems because the guitar impedance level might be a mismatch for the transformer?
Yes, you can't really build a transformer with a 1Meg impedance. Guitars need to see a high impedance otherwise you lose treble and the controls don't work smoothly. The general consensus is that 1 Megohm is a suitable impedance, although some of the early guitar amps had much higher input impedances of up 4 or 5 Meg and many guitar effects pedals go as low as 500K to 200K. Some pedals actually rely on loading the guitar as part of the sound and don't work properly if inserted later in the effect chain. If you knew that you would always have an effect in the chain that was not true bypass and had a 1M input impedance then you might get away with driving the transformers without any buffering.
You could modify the BYOC kit, or buy just the parts you need and build from that. The sightly unusual parts are the isolating transformers and I don't know if BYOC sell those as a separate item. Otherwise you need to source some suitable audio isolation transformers from somewhere. Since you are only dealing with guitar signals the transformers don't really have to be that great in terms of fidelity.
Based on the BYOC design you could route the outputs of IC1b and IC2a directly to the primaries of the two transformers.
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