I always assumed that pods meant increased air flow, hence the upjetting,
That's a common misconception.
1- "pods" isn't a specification. It's a style. Not all pods behave the same on the inside, even if they look similar on the outside.
2 - They *may* help increase airflow at and above Red line RPM. Intake speed is determined by displacement, cam, and valve size until the induction begins to produce limiting factors related to high air speed. At anything below max limits, the actual airflow is exactly the same.
3 - The reason why jetting and adjustments need be changed is that the most pods reduce the carb throat vacuum, which is what pulls fuel from the jet. Less suck, less fuel. To get more fuel with less suck you need to have larger fuel delivery orifices. You can see this for your self. Use a small diameter straw in your milk shake, then a large diameter straw. The larger straw provides more delivery or the same effort.
but using the stock settings for the air/fuel mixture screw (1ish turn out) and even raising the needle jet to the middle notch, I am still fouling out plugs.
Ok, are you saying you ran these carbs with the stock air box and it didn't foul plugs? Or, have these carbs always produced fouled plugs in your experience.
This is sooty dry fouling too, which is pure rich running, but I can't seem to wrap my head around how increased airflow results in running rich.
It's not the air flow. It's the throat vacuum that draws fuel. If you actually increase air demand (volume and/or air flow rate), then the venturi could make more vacuum. But, a filter alone can't make the engine ask for more. You'll need a turbo or supercharger for that.
Just to note there was a puff of black smoke just off of idle everytime which is why I raised the needle one notch)
Perhaps a terminology issue. Raising the needles make for a richer mixture. Raising the needle clip leans the mixture.
All I am left with is that the pods, foam cylinder type, and cheap, are just crap.
I can't argue that, especially for street use.
I hope going back to stock is the miracle everyone says it is.
Miracle? You mean like all the stock units sold with the original bike?

I'm not going to talk you out of the stock air induction system It is superior to 90% of the "for looks" pods.
But, how do you know the carbs are clean (emulsion tubes). What jet numbers do you have? Are they Honda factory items or aftermarket needles? What number appears on them? What is the set up number stamped on your carbs?
How confident are you that the air jets and the internal passageways are clear of corrosion and and other crud?
Restore to stock and it will run well like stock. But, it all has to be in stock configuration.
Um, what muffler do you have?
Cheers,