Here is a forums link for someone who has the same furnace as you and they cleared a blockage with an air compressor I think.
http://www.thorforums.com/forums/f8/...ted-10346.html
Yes it sounds like you have a wiring problem, as the on/off switch in the furnace should turn off the furnace and 12v to the thermostat also. I am attaching the schematics from the manual linked in the above forum response. I think the schematic diagram at the left is correct, but the diagram on the right side might have an error where the thermostat wire from point 5 connects in the diagram. It shows the thermostat wired connecting between the sail switch and limit switch which is wrong I think. The thermostat wire should be connecting to the control board and sail switch. So, that’s a surprise if I am correct. Jpeg of it attached.
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