Why was D1 & C20 burned?
If there's a problem with the board/circuit, it will do no good to replace D1 & C20 to only have them burn up again, possibly taking out other components with them the 2nd/3rd/4th/etc time around.
Use your continuity setting to check for shorts in the power supply.
I'd also go through the board and retrace it while reading the schematic (and relabelling it as necessary).
[EDIT: Just looked at the schematic again and there's a lot of RefDes missing from it, so I'd definitely trace the entire pedal and fill in the blanks.]
Check the two 10k resistors that form the voltage-splitter to get the +4v5 — C20 is just after that voltage divider and would be feeding the OP-AMPs via various resistors, so I'd make sure the 10k/10k voltage divider is working. Of course, the full +9v is coming into the IC via pin 8, but I'm wondering if C20 is burnt out, what things down4v5stream are getting sizzled.
Hmmm there's nothing 4v5 hitting the 2nd op-amp — There's 9v feeding into pin5 via a 10k;
Pin3 is getting 4v5 via 10k while pin2 is getting 4v5 via 4k7/47n combo... I'd check those as well, make sure whatever damaged C20 isn't getting that far.
Moving forward I'd do two things:
1) Remove the IC and install a socket, install a known good fresh IC, but only after making sure there's no power shorts etc. No point in toasting ICs, whatever they cost.
2) Install a 1N5817 between the DC-jack and the board
Going through the circuit in its entirety may be tedious, but it may help you catch the problem or other problems and, at least for me, it's educational — a good exercise.