dirty carb?

My carbed mazda started running like crap, I thought it was ignition so I rebuilt the distributor with new pickup and integrated ecu. Still runs very rough at times, but smooth at others. Im leaning toward a dirty carb now. I looked at opaque filter and its still white, no crap in it. This motor has a recirculating fuel system where the little facet style electric fuel pump pumps through filter, then carb, then most of it recirculates back to tank. It keeps the tank very clean as it always filters the fuel and its always moving so it doesnt stagnate. What would a dirty carb symptom be? It seems to idle fine but at speed, it feels like it has a terrible random miss, then like that, it goes away and then comes back again, totally random. When I come to a stop, sometimes Ill stall, but it always starts right back up and settles to a smooth idle. Im pissed the distributor was not the issue, as I waited 5 days for parts. New plugs, 4 month old cap and rotor, wires OHM out ok, under 6 a piece and this was out of the blue, no repair or anything done to start it or cause it. could my main jets (2) be clogged/clogging or what could cause the truck to drive like this? 10 hour work days and 3 hours of school a night didnt allow me to look at it closer.