My furnace and hot water tank heater shared the same flue vent. I replaced my hot water tank with a tankless and the tankless has it's own direct vent. Now I have a problem with condensation in my flue pipe now that it's just the furnace.How or what can I do to stop the condensation in the flue for the furnace? The furnace is in the basement and the vent goes up two floors (inside the wall) and through the attic. I'm worried this will damage the furnace.

You might have to have a smaller sleeve inserted due to insufficient temperatures or volumes for the size you have now. Best to consult an HVAC expert and get estimates.

You will likely have more chimney damage as a result that furnace damage.

With just one device now, you may not get enough heat to evaporate the condensation. In essence, the flue is too large. A flue that is too large allows too much air to circulate, making it difficult for the warm gas and vapors exiting the furnace to create a strong updraft up and out of the vent. Instead, cold air from the top pushes the warm air down and traps it in the flue. As the vapor sits in the flue it cools, creating condensation.