1. I have the Stoker and I run the top vent nearly closed. In my experience, having the top vent wide open led to run away temps.
2. Yes. I think later versions of the Stoker and other ATCs have a button/setting you can employ when opening the lid that takes care of it automatically. Check your user manual.
Also, I found that having a work space nearby and the Unknown BBQ Hinge installed really helps avoid temperature spikes. Now, when I wrap, the lid is only open for a second or two.
3. Nope, standard minion, but the amount I light depends on my temperature goal.
Also, no need for water in the water pan, unless you are cooking something like a Franklin BBQ style brisket that calls for water.