I think it is possible that the C17 cap could be a part of the problem. To weed out the potential that your noise is coming from the Tremolo, you could remove C17 and see if the noise goes away. The symptoms you seem to be describing are not A typical of a bad cap, but a bad cap will do all kinds of strange things to a circuit including but not limited to crackling, popping, and other strange behaviors. It upsets the bias ( in most cases ) of the preceding circuit and this can cause the preceding circuit to go into cutoff or depending on how the cap failed, it can be any number of things that happen. In the case of a tremolo, it is an oscillating circuit that shifts bias in order to create the effect. That circuit in this case is connected to one of the PI's two primary inputs. Since the Tremolo is already acting weird, I would suspect that is the problem circuit. A way to test that theory is to remove C17 ( in this case ) to see if the problem goes away. You should not hear ANY remnants of the tremolo circuit at all with C17 removed. In which case, if your noise problems go away too, you know that the problem is in the Tremolo circuit for sure. I would assume based on the symptoms that the problem is because of a bad capacitor, and or in the switching circuit for the Tremolo. The tremolo not working when it should be, but only just audible at very high volume settings can mean the switching circuit is bad, or simply the bias shifting of the circuit has gone bad. The bias shifting of the circuit is created by the capacitors. Typically the only reason to change those capacitors is to alter the rate of the tremolo. The depth is controlled by resistance/pot, which can also be a failure point. The C17 cap you changed at the end of the Tremolo circuit likely has nothing to do with the actual functionality of the circuit and is only there for DC-decoupling and to potentially set the amount of bass the circuit will pass onto the next stage. A 100nf is larger than a .047uf cap and would allow all frequencies of interest to pass through, BUT, the Tremolo circuit doesn't pass audio per se, it shifts bias. So that change made at C17 to me would be a fruitless one. I would put it back to the original value.
Not saying this is what I would do, but If you don't care for Tremolo at all, removing C17 will rid the circuit of use and if that solves your problem, you could simply leave it that way? The schematics addition of having voltages is really helpful. You can test against that and probably nail down where in the Tremolo circuit the problem is located. Again, I suspect a failed capacitor, but that is just a hunch. I would weed out all other possibilities first before I shotgun a full circuit capacitor change.
Not saying this is what I would do, but If you don't care for Tremolo at all, removing C17 will rid the circuit of use and if that solves your problem, you could simply leave it that way? The schematics addition of having voltages is really helpful. You can test against that and probably nail down where in the Tremolo circuit the problem is located. Again, I suspect a failed capacitor, but that is just a hunch. I would weed out all other possibilities first before I shotgun a full circuit capacitor change.