With noise present on an output pin, it's likely the 4013 output has disconnected.
The note that it has to be a Motorola suggests something is different about them. There was a time when there were many versions of these logic parts that had specifications particular to the manufacturer. Now there are far fewer choices and the Moto isn't one of them. You may find the clock waveform even less square with a modern replacement, especially at the highest clock frequency. We will hope it's not a problem.
If it came to it, the dual transistor could be replaced with a little adapter board with a pair of matched hfe NPNs like 2N3904 stuck face to face. I don't think this application really requires perfectly matched tracking between the two transistors as it does in a VCO pitch CV converter.
Well, put in a new CD4013 and still the same issue, no flanging at all.
I tried replacing some of the C945 transistors with no help.
I didn't have any A733, and 2SA1015 seemed close enough so I tried one of those, but no luck either. Should I try to get real A733's or should the 2SA1015 be okay?
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So the last 2 main things to try would be the dual transistor, and then the SAD1024 bbd.
As a test for the time being, could I just breadboard a couple 2N3904's and put temporary leads to the solder points? Basically if they don't match at all, would the effect still work, just wouldn't be sort of "calibrated" correctly? I also have some KSC1845 that seem like they could work, and they also have center Collector, so I just would have to solder the emitters together.
The other option is buy a $150-250 pedal to grab a SAD1024 (obviously don't want to do this unless I definitely have to. Is there any way to test that it is the SAD1024 (specifically pin 10, which currently is the only obvious issue I see, as it isn't receiving a clean signal from IC13 of the 4013).
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Unfortunately it is just getting worse and worse, as this PCB is becoming a brittle mess, haha. The traces lift soo quickly and break off, as if I'm using a welder instead of a soldering iron. I've had to bend numerous leads to solder past failed pads, but I always check continuity between components. That being said, this could be something very small and annoying. I've built tons of pedals, a Buchla Easel, and many polysynths, so I'm not a total novice, but that doesnt mean I didn't make a mistake.