So, I'm not really understanding what R5 and the switches do.
You do not *need* to use them; they're just there to make sure that if you do need them, they're available.
The first firmware I'd write would use R1, R2, and R3 potentiometers (and the pedal). R1 would control the pulse rate (between say 0.2 and 2 seconds), R2 the duty cycle (between say 10% and 90%), and R3 the off-time current (as a percentage of maximum).
However, if you find that you want to add those other modes, or add a three-button menu interface (up, down, and select), you need those three buttons. And you still have one potentiometer free. You might want to use it for decay rate (so that when you release the pedal, the welder always sees a smooth easing at that rate).
It is horrible to find out you created a board that you cannot use, and must redesign. I like to have a bit of future-proofing.
R4 is still the potentiometer inside the pedal? Or does that correspond now to the Pedal_A, B, and C inputs now, leaving two potentiometers on the board for something else?
The pedal potentiometer is connected to Pedal_A, Pedal_B, and Pedal_C, and the pedal switch to Pedal_D and Pedal_E. There are up to five control potentiometers (knobs) you can connect to the Pro Micro in addition to the pedal.
I'm guessing the resistor still needs to be on Pedal_B P3 and on the switches as well, like in previous schematic.
The Pro Micro does have internal programmable pullups, so they're not really needed. You can use standard pullup wiring (switch between ground and a 10k resistor to VCC, and input connected to the point the switch connects to the resistor), which protects against programming bugs. Debouncing capacitors can be used in series with the switches (because at microsecond scales, the switch does not change states cleanly, but bounces a few times between open and closed), but that too can be done in software.
So the capacitor bank for machine input, those are electrolytic, or all 1uF and below ceramic?
I am not certain; I'm not even certain on how much capacitance is needed to get comfortable results. Remember, the existing pedals use capacitors with very high voltage ratings. I do not know if that is for compatibility, or actually necessary with all machines. I would personally do a compromise, and find capacitors rated at say 450 V.
As an RC filter, the break frequency when using the capacitors shown, would be around 15 Hz. At 50% duty cycle, the peak-to-peak ripple would be around 0.1%. Is that enough? Is that overkill? I do not have enough practical experience to know; as I said, I mostly use digital sensors myself.
What If when I design the board, It's all one board, but I separate them with a slit routed in it
That helps with isolation, sure. I was thinking of using a separate board more for ease of putting into an enclosure (you could put the capacitors on both sides of the board. I like Hammond diecast enclosures, and you could put a conductive separator (plate, or just circuit board material) to help with the EM noise. I don't know if that matters, but that's what I'd do.
I was planning on using a TP4056 tied to a 18650 3.7v battery, with a step-up converter to get to 5v for the arduino (or just use the tp4056, battery, and step down module to 3.3v arduino), then just have the USB connector sticking out of the project box for recharging the battery. That battery should last months on a single charge on this simple circuit, i would think.
OLED and Pro Micro do consume quite a bit of power. Haven't measured it, but if it was say 150 mA on average, I would not be surprised. A 2000 mAh USB power bank (a single 18650 cell, from a reputable local seller) costs about 5€ here, so would provide about a day of continuous running. I think it would be easier if you had a short USB cable with a male connector sticking out from the enclosure, and a couple of those cheapo power banks, and simply switch them when they run out; keeping the other in a charger.
That way you could have a power switch on the enclosure, too between the two ends of the USB cable; one end sticking out, the other end inside connected to the Pro Micro. Ferrite bead or a choke where it exits the enclosure. KISS.