When you increase the displacement of an engine, assuming no other changes, you increase the volume of air being drawn though the carb throats. This increases the vacuum (decreases the air pressure) seen on the outgoing side of the fuel jets relative to the atmospheric pressure, and causes more fuel to flow through the same jet orifice.
Stick a straw in a drink don't you get more drink if you suck harder?
Pod filters usually reduce some of the resistance to draw at the mouth of the carb and bring the carb throat pressures closer to outside atmospheric, thereby causing less flow throught the fuel orfices due to decreased pressure differential across the jet orifice boundary.
If pods have the same pressure differential resistance curve over the entire RPM/ airflow range of the motor relative to the stock filter, you can adjust overall mixtures with the pods. If however, the resistance to airflow is not a direct relation ship I.E. a differential pressure at different speeds relative to the stock filter, then some aspects of carburetor jetting will have to be changed. Maybe just main jet, maybe just slide needle position, maybe just slide needle taper, maybe all of the above, or any combination of the above. I view the pods as a Hail Mary attempt at adjustment. Might work. But, you may just have to rejet and readjust carb settings either way.
I also don't understand why you are re-honing the cylinders after just 1000 miles. Yes, if new rings. But, if what you have hasn't been damaged, just put it back.
Cheers,