Here are you first suggesting to add a 1M back to 4.5V and also change the 22nF to 47nF? I just want to be clear - I understand the second option.
Correct.
Currently the 22n and 1M form a high-pass filter. The -3dB cut-off frequency is f = 1/(2*pi*R*C). When the second 1M resistor is added the capacitor will see two 1M resistors in parallel. Rparallel = 1/(1/1M +1/1M) = 500k. That raises the cut-off frequency so the cap needs to be increased. The second option uses 2M2 and the two 2M2 resistors in parallel results in a parallel resistance of 1.1M so it doesn't change the cut-off.
The multimeter I have right now is relatively inexpensive, but I also read that some 1M multimeters can still be accurate, or at least readable if you account for the input impedance - looks like an upgrade is in my future!
I'll admit a 10M meter is nicer to use but on occasion you still need to account for the 10M input impedance for accurate results . For example your 4.6V might measure 4.2V. So it still looks off, but by less. You can learn to spot loading issue and know when to correct the reading.
A trick to avoid meter loading problems is to first measure the point and convince yourself there is a voltage there (not open) and that the meter is roughly the expected loaded reading. The next step is to accurately measure the 4.5V reference voltage. Then measure the voltage *between* the 4.5V reference. You need to place the meter's negative lead on 4.5V reference. If all is well you should read zero. The accurate reading is Vaccurate = "V 4.5V reference" + Vbetween_reading. If you get close to 0V for the "between" reading you know the point you want to measure is in fact 4.5V and the first measurement was low due to meter loading. While it takes some words to explain it is easy to do in practice, all you want is to see a zero measurement.
So here you're suggesting to remove those as the unitary gain amp and basically just use the TL071, is that correct? This is in lieu of adding another 1M to 4.5V and changing the 22nF to 47nF since you're removing them of course in this case.
That's correct it's another option. It completely removes the biasing issue of Q1. The TL071 has sufficient drive to drive the output on its own. The 1K resistor on the output of the opamp is a wise addition as it prevent the opamp oscillating when driving a cable. Sometime you add a JFET buffer for sound but in your case it's causing trouble because the tone controls boost the signal after the clipping diodes.
For example, I knew there was a biasing issue somewhere (because I read about it a while back - in the debugging), but I didn't know how to fix it. To use a personal metaphor (20 years in the food service industry), it's the difference between following a new recipe to create a dish and hoping it turns out alright, and following a recipe and running into issues along the way but knowing how to correct for them to still offer something delicious. Time and experience are the obvious answers, and I'm in no way looking for shortcuts or a bridge across, but I am looking for any stepping stones to help me along my way.
You sound like a switched on guy. I can tell you electronics *is* exactly like that. The easy approach to electronics is to have an idea of cause and effect. You see a problem then you need to counteract it. It does take time to build up your library of "thought tools". You can do a lot of calculations to calculate the expected voltages but that's a whole different level (perhaps like trying to calculate the
increase decrease(!) in PH from adding lemon juice).
So for the JFET.
- The problem in you case is the source not sitting near the middle of the supply so the output voltage it can't swing much in the negative direction.
- You want to raise the source voltage.
- The solution is to raise the gate voltage. That's how JFETs work. Raising the gate voltage will raise the source voltage.
- Next is how much. You want about 4.5V on the source and your source is at 1.9V so it needs to be lifted 2.5V.
To raise the source by 2.5V we *roughly* need to raise the gate by 2.5V. It's not quite like that as when we raise the
source voltage more current flows down the the 10k source resistor and that changes the voltage between the source and
gate.
- Currently your gate is at 0V. By connecting the gate to a DC voltage source via a resistor we form a voltage divider between
that DC source and the gate.
Here,
Vout = Vin * R2 / (R1 + R2)

In your case the added resistor is R1, R2 is the existing 1M resistor R15, Vin is 4.5V.
If we add a 1M resistor we get Vout = 4.5 / 2 = 2.25V, which is close enough to the 2.5V we need.
FYI, there's a few common biasing schemes for JFETs. Which one to choose depends on depends on the JFET. The JFET has a parameter Vgs(off), loosely called the pinch-off voltage VP. VP can be anything from 0.25V to 10V for different JFET models. The voltage difference between the gate and the source is strongly affected by this parameter.
The gate will always sit between 0V and VP below the source.
The first scheme is your original circuit, that's the simplest circuit. However where the source ends-up is almost entirely determined by VP. If you want the source to sit at 4.5V you need quite a large VP JFET. So this form of biasing limits your choice of JFET. Only a few JFETs work optimally like this.
The next simple scheme is like the Boss circuit. Here the gate is raised to 4.5V. You want the source to be at 4.5V but you know the source is going to be at a higher voltage than the gate. In this case you want a low VP JFET so the source isn't too high. With modern JFETs which tend to have low VP's this is quite common.

Another form is to bias the JFET with its own resistors. When the two gate resistors are equal this more or less operates liek the Boss circuit. The difference is the 9V supply can be noisy whereas the 4.5V rail is usually quiet.
The advantage of this scheme is we can tune one of the resistors to tweak the gate voltage to get the right source voltage. The extra resistor gives us the freedom to play with the voltages.

For your JFET the VP isn't quite high enough to get good performance from the simple circuit, as you found. However the VP is a bit too high to work properly in the Boss circuit. The circuit I suggested lifts the gate just enough and the added resistor connects to 4.5V which is nice an clean. So IMHO it solves the problem and has little side effect. You probably won't see this form of circuit very often.
As for bypassing the JFET altogether. The thinking behind this idea is simple, the opamp can drive the output and there's no real need to for the buffer.