i should point out that the inline filters can cause bad flow problems even if the petcock is perfectly clean and flowing from both nipples. mine sometimes get air trapped below the filter, which seems to have a hard time travelling back up through the filter and into the tank. i just flushed my tank out again recently and completely rebuilt my petcock (new screen/tube assembly and thorough cleaning of the lower body), and i am still having flow problems every once in a while. when it happens to me, my bike suddenly runs exactly as you describe: it seems like it's running out of gas to two of the cylinders.
when this happens (usually when i sputter in between running out of gas and switching to my reserve), i can squeeze on the fuel line going to 3 and 4, and actually force the air back through the filter. amazingly, sometimes it will run fine when it looks like there is no fuel at all travelling through this air pocket (it must be trickling very lightly), but i have to believe that this will affect high RPM fuel needs.
in any case, inline filters suck and are extremely problematic. it helps to make sure that they run "downhill" the entire way to your carbs, helping to eliminate air pockets.
but i think you have dirty pilots anyway...