I always used a water pan with both stackers that came with the unit. Used regular Kingsford charcoal briquettes. Filled the basket to the top with a bit of a hole in the middle, where I'd pour a full chimney of lit coals. Not sure what you mean by fuel source.
My bad, fuel source and fuel type...same meaning. As for that water pan, are you adding water or any liquid to it? Try it with no water, and see if you have better results. IMO, liquid of any sort in the water pan adds little if any moisture content to the end product and just makes your fuel work harder to maintain temp. Just my opinion and you'll find a lot that disagree with the idea of a dry water pan.
You might also consider losing a stacker if you are doing a cook that will allow you to get all the meat on one grate. We've found on the two occasions that we have cooked with 3 stackers, that the top stacker was highly inefficient. Regardless of how many stackers you utilize (well, at least 1, 2 or 3...never cooked with 4), it seems that the grate level temp has a differential of about 10-20 degrees, top grates being the cooler. In short, if we dont need an additional stacker to hold additional meats, we don't use it.
You also might want to try using some aluminum tape to shut down air entry around the doors. We have done this on occasion when it has been windy or cold. Works like a charm and really adds that "white trash" aspect to your cooker.

As for the Pro Q's paint fading...that's one of the few drawbacks that I haven't been able to work around. Ours still cook great, they just don't look great. I've been really lucky to not be afflicted by the prettier/bigger/better smoker syndrome.