Dear Richard,
I am trying to figure out how the output side of this circuit is supposed to work. When driving a TE cell, you want to minimize current ripple because spikes in current cause losses in the resistance of the cell as a function of the square of the peaks of those spikes, making the cell less efficient for cooling (has more internally generated heat to deal with).
Thinking "out loud" here... let's see... Yikes! Q2 is an 80 A MOSFET! How big a TE device are you driving? Oh, I see, this is a buck converter with the switching on the negative side of the voltage source. The duty cycle determines the voltage that will appear across C4, ranging from about 0 to 13 V as duty cycle ranges from 0 to 100 %.
You do realize that the common-mode voltage of your PDRV output terminals will vary from 0 to 13 V at your switching frequency, yes? The PRDV terminals are only connected to the TE cell or resistive heater, right? No additional tie to GND? (It is unfortunate that your schematic for Q2 does not also show it's body diode, although I don't think it ever commutates on during operation of this circuit because there is nothing to push the voltage of PDRV- below GND.) This common-mode voltage is why your output voltage waveforms have so much "noise" on them. That is not noise. It is real. You need to read them differentially to see the voltage appearing across them. Shy of a true differential probe or isolated probe, you could take the difference between them by referencing two scope probes to GND and taking the difference in software. Don't know if your USB scope can do that, or if it is fast enough for 97 kHz switching.
D1 is a key part of the buck regulator. When Q2 is on, it pulls PDRV- down to GND. PDRV+ follows suit, albeit at whatever voltage is across C4 at the time. This causes current to build in L1 and voltage to rise across C4 and the load. When Q2 turns off, the current in L1 continues to flow down through C4 and the load then finds its way back up through D1 and to L1. This causes current to decrease and the voltage across C4 and the load to fall. Note that when this is happening, the voltage of PDRV+ is higher than 13 V by whatever the voltage is across the load and C4 at the time. Which means that that voltage also appears across Q2. But Q2 is rated for 40 V so it should be good with the 26 V (plus diode drop) it might see.
Now, I see that D1 is a Silicon Carbide Schottky rated at 600 V, 24 A. We must be careful here to note that the current flowing through the load is the average of the current flowing through L1. But peaks of L1 current flow through C4. All that current flows through Q2 when Q2 is on, none of it through D1. But when Q2 is off, all the current through L1 also flows through D1. Depending on the duty cycle, the average D1 current can be quite small or it can be nearly equal to the load current. The peaks of the current ripple will be higher than the ripple midpoint or average load current.
Do you know how much current you are driving through your load? You need to make sure you are not over driving D1. Remember it carries all the load current (and then some peaks through C4) for part of each switching cycle.
Regarding isolation. I think Peter's point is that since you are powering both the input and output sides of the opto from 13.0V and you are referencing the input of the opto to GND, you are not getting any isolation between input and output. To achieve isolation, the input should be powered from a separate power supply on the other end of your several feet of wire and with no connection between input and GND. One advantage of the opto is that it provides a stiff drive for the Gate of Q2. If you got rid of it you would still need a robust gate driver chip.
A scope would really help here. I've not used a poor-man's USB scope so I don't know how limited they are.
But I would think that referencing the scope probe to GND and probing any pin on the opto should give you a better insight into what is happening to the opto. And you should be able to see the output of Q2 (PDRV-) as well. You have to make sure your PC and USB GND and your circuit's GND are all tightly connected to each other and nothing else is connected to GND (no GND loops). Or put A USB isolator in the USB link to separate the PC GND from the setup.
I hope this helps and you can figure this out.
Best,
JD