I have only done peppered stout one time and if I remember correctly it was about a 7hr cook with the smoke phase running at 250 then in a pan with onions & peppers and wrapped with foil at 350 until IT hits 200ish or probes tender. The last phase was 1 1/2 - 2hrs to reduce liquid, I think. I have done plenty of pulled beef which is basically the same cook minus the liquid reduction and a 3lber will take about 5-6hrs
@henapple should be along before long, he is the resident OO guru. It does sound like you might have a build up in your egg. I am not one for the wide open, ballz to the wall clean burns but rather hit it at 600* and let the lump burn out. This way works for me when I get a build up of crud inside the egg.