With our Stoker and LBGE, the fan runs about 2 seconds every 30 seconds while maintaining anywhere from a 250-270 grate temperature.
Where are you placing the pit probe? If it is placed too near the meat, it will lower the reading and cause a higher cooking temp (at least until the meat comes up in temp to minimize its effects on the cooking environment).
Do you have the probe placed over the "vents" of the plate setter (i.e. outside the circular portion and not above the leg supports). This will give you an erroneous reading as well. Generally, I try to point the pit probe towards the meat or parallel to it about two inches from the meat and 1.5 inches away from the circumference of the plate setter, preferably over the legs of the setter to protect the probe wires. This can be tough to do with big cuts, but I try to balance the location as best I can.
What dome temp were you seeing with your stoker running at a steady state temperature? Generally, we see about 50 degrees warmer on the dome temp compared to the grate temp. This is most likely due to the natural convection of the dome flow around the plate setter. Many of our recipes had to be adjusted for time when using the stoker. IMO, this is due to the stoker maintaining the desired grate temperature ignoring the dome temp whereas cooking without the stoker results in a desired dome temp. Simply put, when you are using the dome temp probe, the temp the meat sees on the grate is lower and results in a longer cooking time.
For most low and slow to medium temp cooking, we set the daisy wheel at about 50%. This provides a free flowing situation for the fan back pressure, but not so much as to create a flue effect on the fan damper and lose control of the temperature. If the daisy wheel is open too far, I have seen it where the natural flow through the dome, will pull the fan damper open slightly and allow the temperature to creep up without the fan running. It's ok for the fan to have a bit of back pressure. It simply means the fan will cycle more often and run longer to "force" the air into the dome in order to maintain the temperature. I like to hear the damper rattling occasionally; it lets me know everything is cycling and working correctly without getting out of my chair.
As for your convection oven concerns, 5 cfm is barely a breath of air compared to the volume of the dome. I've not noticed any effects related to this unless the meat is near or in the plate setter "vents". This will cause accelerated cooking of the portions hanging in the flue flow. Of course, this happens with or without the blower fan.
I do not use a water pan as I do not like the steaming atmosphere it creates and how it effects the bark. You may already know this, but if you choose to use a water pan, the fan will cycle more often and longer to maintain temp and you will consume more charcoal.
Hopefully this helps. Congratulations on the stoker. Once you get her dialed in, you'll love using it.