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Why are you soaking them so long? The reason for soaking (as I understand it) is just to keep them from flaring up. Soaking that long would probably bleed all the flavor out of them too.
The answer is yes....you can use Traeger pellets in the MES...they will produce quite a bit of smoke at first but then settle down to a nice medium smoke.... you don't soak pellets at all...
I usually onl;y soak may chip a few minutes before use....I have had no problem with flare up and they produce a good emount of smoke..!
When I use the wood chip tray on my MES I use just a very small handfull and usually end up putting more in every 20 to 30 minutes. I try not to use a lot of chips and I never soak them. If you think about it... the heat just dries out the wood chips and they start back where they would have been before you soaked them. I tried the soaking thing when I first started out smoking and I just never saw the advantage of soaking. An added step I eliminated from my method.