I haven't used it yet in parallel with an actual hot cook, but it seems like you're going to have to re-adjust your top vent settings for whatever temperature you want for the cook, as you're introducing a lot more air in the firebox - whether the pump is running or not. Hence, I'd recommend removing it from the KK if you're not actually using it for smoking.
As far as cleaning goes, I don't intend to clean the inside. Just wipe off the outside so it stays nice and shiny and dump the ashes out the bottom. If you keep the flow tube upside down (opening facing down), it shouldn't get clogged up. Time will tell.