When you cleaned out the flue pipe, did you also clean out the grates? The holes will often get filled up and need to be cleared out in order to get proper coal bed air flow. Also, on many stoves there are baffles up top in the burn chamber and/or C-channels on the back wall of the chamber which carry vent gasses out to the flue. Make sure those are both cleared of fly ash too.
Next, what is your MAX value set at. On LL stoves it should usually be set between 40 and 50. Sometimes it's outside that range for optimium, but 45-46 is a safe starting point.
By increasing the MIN value you increased the feed rate while at idle (FR 0). If you're not at setpoint that should not be where FR is at, though. What is your FR screen saying?
Lastly, it is possible, with the very cold days we've been having lately, that your chimney is over performing and pulling a lot of hot air out of the burn chamber. A damper can be helpful in exceedingly bad cases, but usually a barometric damper is all that's needed. This will automatically open and close as needed to supply excess chimney draft air from the room, instead of pulling it out of the stove. Your stove should have had one included when you purchased it, I believe.
AS to the bad temp reading on the coal-trol. There is a way to calibrate it, but it's limit is about 10 degrees of calibration adjustment, so you may well be over limit to get it right. The fact it is that far out of whack is not right. I'd suggest you call our shop at 315-299-3589 to discuss your options. We have a three year warranty on our product. If it is over that period then it probably makes sense to do a repair as opposed to buying a replacement thermostat.
The calibration is done by pressing and holding the MENU button for several seconds, until it reads out a set of alternating screens that say "A ###F" and "R ###F". R is the raw temperature reading, unadjusted. The A value is the adjusted one. Use the UP and DOWN buttons to apply adjustment. You may find you need to use the DOWN button to increase the adjusted value up. I know, it's backwards. There's a logical reason, but that's a story for another time.
Once you're adjusted it, tap menu a few times to exit the advanced menu and get back to the round robin display.