Through all the difficulties I have had with my 550, I have resisted reinstalling the original airbox, filter and plenum because it's such a pain in the patoot. I had re-jetted and re-jetted, and finally got the bike to run reasonable well, perhaps a bit hot, with pods. Last weekend I had the carbs off yet again for some thing or another, and all those mentions of burned-through pistons and perpetual poor performance began to replay in my little BB-sized brain. . . .
I dug out the box that contained a nearly-complete 550 airbox and a raggedy old filter, probably the original one. Located the original 90 main jets. Two hours of struggling later, I had the carbs and airbox back in factory configuration, with a cardboard cover that approximates the one illustrated in the manual. I had installed a brand-new set of size 38 slow jets earlier, and idling was already a bit better. But when I started the bike, it just seemed to feel better -- smooth idle, clean throttle response with no lag.
So -- to Two Tired, Duanob, Dave500 and all the others who talked me through the first months of SOHC4 ownership, I offer my sincere thanks, and declare that you were right, I was a dummy, pods mess things up. A more experienced tinkerer can surely make a SOHC4 engine run like heck with pods, but noobs should avoid changing too many things at once. Stick to the basics and learn from the old hands.