I don't think you've missed anything. I had the PUGS on, and the canvas zipped up probably 90% of the time. The smell may eventually dissipate on its own but as mentioned it's really strong this time, and this is 3 days after coming home. I would describe it as the smell you get after putting a campfire out with water...smells like burnt, wet wood.
And no surprise but DW's hair smelled like smoke for a few days after, as did our clothes, though we can usually correct that with one washing.
I have opened the bunks back up, and will try the vinegar trick today (don't have any charcoal). Failing that, DW has lots of Yankee candles we can burn, so masking the smell can certainly be achieved, hopefully longer than temporary.
Btw, we had guests who had never camped before, and they loved how dark the PUGS kept their bunk end. If it weren't for the 50 generators firing up around us at 7AM they'd have probably slept half the morning lol.