Some extremely puzzling measurements. Some contradict others. I'm having trouble trying to match them up to a fault!
which I think is designed to be ~4.9v.
Yes it is actually higher than 4.5V.
With the pedal on, the junction of R39-R46 reads 0 volts. The opposite side of R49 reads 8.6 with a battery.
Very odd to get 0V. As IC1 pin 1 and IC1 pin 7 could not get to the measured voltages with 0V on the R39-R46 junction. I'd perhaps try to remeasure that voltage.
I tried testing both R39 and R46 but couldn’t get a reading for either. When I switch to the closed circuit tester, they both test as an open circuit one direction and closed the other. I think this means that R46 is bad and acting like an open circuit so that I am really only testing D1 when I try to measure the resistors. However, I cannot convince myself that this is correct since then R39 would be separated from D1 and I should be able to measure a resistance.
You have to take in-circuit measurements with a grain of salt. If you get crazy measurements it's a good idea to reverse the multimeter leads to see if you get the same crazy measurement, or a different crazy measurement. Often the caps take a while to charge up or they hold charge from being previously powered. (You have got the power off, no battery and jacks removed?)
Having said that there could still be a problem in that area. Maybe measure across R39 and across R46 when the device is powered. In both clean and effects modes.
Starting from the most basic measurement IC1 pin1 looks OK. However IC1 pin 7 should follow IC1 pin 1 but it is way off. I can't see how that can be the case unless IC1 is blown or you have some sort of short or cut-track on the PCB.
When you take your measurements, what ground point are you using? Note the DC jack -ve connection is not ground there's a resistor and diode (R17 and D3) between DC jack -ve and ground. So the ground point must be the circuit side ie. the ground on the jacks or PCB.
If you ground is correct maybe measure along R8, R9 and R5. Maybe also pins 2 and 3 of IC1.