I'll try to extrapolate a little bit though articulation on the dynamics of the burn is NOT as easy as discussing exact, acceptable installation dimensions, materials, clearances, etc..
Because one person waits for the secondaries to kick in before reducing primary air certainly does not mean that I see secondary burn unless primary air is reduced. And some will inform you that if your glass is clean, you are burning hot enough and with seasoned enough wood. They will also be the same ones who offer special concoctions for cleaning your glass.
It's 35 degrees out right now and I seem to be having trouble getting my stove up where I want it. It's not windy. My wood is below 20% moisture level and I have a good bed of coals. What is different is that this load conists of many small chunks and end pieces which are not normally burned. This is just another example of how easy it is to change the dynamics of any particular burn cycle.
But in staying with the topic of thermometers I offer this; For me, and I speak only for my situation (as you will become familiar with your own), the flu temp will not always dictate the actual stove temp that I want before I start to close down the primary air which "sets" the secondaries and gives me the prolonged, sustained temperature burn, required for my conditons at that particular time. With a stove temp of 300-450 degrees, my flue temp will read about 300 degrees once the primary is slowed. On the other hand, the flue temp may read just about anything, depending on conditions, before I know what the actual stove temperature is.
On my stove, again, my stove, and within the dynamics of my set-up, my secondaries will kick in at 300 degrees stove temp, only with the reduction of primary air though. Depending on the outside temperature, the load of wood, etc., this may be sustainable throughout the entire burn or not. These are some of those, way too many, dynamics which each person comes to learn for their own stove if they want to.
By manipulating both stove temp, and flue temp (using the by-pass mainly), I can get the maximum results my stove has to offer. It certainly is weird getting used to, but is already becoming second nature for me after only eight years (just kidding).
Wow, that hurt my head. Hope it helps!