Is this Flue Temp Probe Full of "It"?

This is very interesting. I hope this is the right place to ask my question, since it relates to thermometer accuracy and placement.

My questions first, then the backstory:
Where should my thermometer(s) be? I have a Rutland and I just got a Condar ChimGard Stovepipe thermometer
Should I have my stovepipe cleaned out and/or inspected before firing up again?

The backstory:
Earlier this week I was happily reading in my favorite chair next to my Petit Godin when I happened to glance over at it and the stovepipe going from the back of the stove to the chimney pipe was glowing red hot. I freaked! Well, I jumped up and shut down the air and things cooled off pretty quickly. Install was all up to code by a pro in November 2009. It uses an existing fireplace.

I have a Rutland thermometer that I keep on the front of the stove near the door. It was reading about 450-500F at the time. So does that mean that the stove pipe was actually half again as much? Yikes! I was burning well-seasoned wood (may have been cedar) with some bituminous coal mixed in. The Godin is made for coal. The air was all the way open since that's what it takes to get a good burn in the 500F range, or so I thought, but I think I've been mistaken because of my thermometer placement. It's been on the front near the door.

I'm wondering if I had the thermometer in the wrong place on the stove. I've read through the posts here and other threads about this, and alot of folks keep their thermometer on the top. Does that mean on the top where one would put a steamer? The Godin is cylindrical and there's not much room on the top if I put the steamer on there. Plus, you have to open the top to refuel, requiring removal of the steamer (and the thermometer if it's there).

I haven't dared light another fire since this happened. I did buy a second thermometer--a ChimGard stovepipe thermometer. I figured I should probably have one on the stovepipe itself, as well as on the stove.

What do you all think--should I have the stovepipe cleaned out before using it again? There's a T-connection with cleanout. I haven't done it myself but the installer said it was easy and that I could do it, although he didn't mention how often. This is my second season, and I have not cleaned the chimney since the install last November (2009). I don't burn every day, and the season here in Central Virginia is not as long as up north. December-February, I'd say. The install was by a pro, and the chimney pipe (the one going up the chimney) is ceramic lined. The stove pipe (horizontal from back of stove) was silver at first, but now it's been discolored from use. It is not black. I don't know if it's double or single walled, but I will find my work order and find out.

It's really cold here, and I miss running my stove (and hate running my heatpump so much!) But safety first...

Apologies for the non-technical lingo. I'm still learning. I look forward to your thoughts and advice.
-Julie