I also have a 40" MES, a little different model 20073012. I've not had any smoking issues like you've described.
If the unit is not yet 1 year old, and if you still have the original receipt, call Masterbuilt and they will send a replacement box.
They're customer service has been very good.
I purchased the Masterbuilt cold smoking attachment and this works very well and was designed for the MES.
A true set it and forget it for at least 6 hours.
I know it doesn't solve your smoking tray issue but,....would take care of your smoke issue.
The A-maz-n smoker tray will not work in this unit. I've tried the AMNPS tray every way possible.
There is just something different enough with these 40" MES that will not allow enough air in to keep the pellets going.
Hope this helps.