Welcome to the site Ken01. I stumbled onto this site in January I think and have found a lot of information and ideas, as well as shared some of my own ideas and experiences in hopes it will help someone else.
On problem #1, I would venture to guess a bad thermostat probe?? I'm running a E-2300 but I've not seen the probe or even where it is. But my reading is within a degree or 2 of my inline thermometer. I am also running (just starting this year) a Wood Doctor HE10000, a little bigger unit but a very different setup. I got it used and it had sat cold through last winter. On that unit the dial temp guage on the front reads about 200, the aquastat is set at 215 but the actual water temp range is on at 180 and off at 190. I plan to get a new dial guage and a new digital aquastat for next season instead of the regular dial type in it now. I want to know exactly what the aquastat is reading.
On problem #2, I have also experienced the backdraft. The WD10000 uses a negative draft to pull air in (draft fan in the chimney). No air box like the 2300 and 2400. Just a 4" pipe from the doorway down to near the floor of the unit that the air is sucked up through. Sometimes I see it "PUFF" a cloud of smoke out that pipe. Sometimes it's worse and even shoots a flame out the pipe. That's a bit un-nerving.
Now, I had never had it happen (to my knowledge) with my 2300 until I made a change to my primary air channel a couple of months ago. The original design was badly cracked, separating from the sidewall and completely full of ash and creosote blocking my airflow to the firebox with no good way to clean it out. So I cut out the back portion of the air channel and used pipe up to the ceiling of the firebox. Unit burns much cleaner but I was noticing the puffing. Restricting the primary air flow has helped a lot. By replacing the air channel the way I did, it had no back-pressure slowing down the airflow after the solenoid as the original design surely did. But lowering the solenoid helped. I was also at the time burning small split very dry wood. Some other guys out here commented on overly dry wood being a cause of this and again I saw the suggestion of restricting the air supply a little bit while burning extra dry wood. I've also limited this from happening by letting the unit burn down to coals, add about 2 arm loads of the small split wood in first to help replenish the coals and make sure it is burning hot and finish the fill with the lesser dry, bigger pieces of wood.
Hope this helps a little.
Jeff