Instead of plugging the bottom holes completely, I used a couple washers with a small hole and covered the large holes under the tray. I use some hi-temp silicone to stick them to the pot. The reason I like the washers better, is instead of cutting off the air completely from the top holes, it regulates it. With the holes completely covered there is actually too much air coming up from the bottom of the pot. This works great for blowing the ash out of the pot, but you are also blowing the pellets out before they are completely burnt! You will also notice that your flame is extremely tall, and your exhaust is a lot hotter. The side holes help to concentrate the burn, in the center of the stove, allowing the stove to absorb the heat, and the pellets to burn completely. With them closed off completely, you are sending a lot of that heat, strait up the chimney! This is what I have found, anyway.
I'm not saying this may be the case, but im not convinced this is sending more hot air out of the exhaust. I look at it this way. The stove is exhausting the same amount of air whether you plug side holes or not. Plugging the holes just means that you are forcing the air to take a different path. Yes the exhaust air will be hotter but thats because more of the pellets are getting burned completely, instead of just piling up as a giant mess in the burn pot. While some of this hotter air is wasted through exhaust, some of it is also absorbed by the stove and radiated while some is picked up by the heat exchanger and blown into the room. With the holes unplugged, and some pellets not completely burned, even more heat is lost because you scoop the pot and throw that heat away (or in your garden or use it for traction on ice etc).
I do notice the flame is extremely tall, I am seeing hotter temps. I am heating the house with less fuel and i am also seeing a cleaner burnpot and no unburned pellets. What i am no longer seeing is clinkers.