I kinda figured that was your thoughts. But I don't believe high efficient's are designed to exhaust out a roof stack as the temperature of the exhaust gasses is much lower. Besides getting a hole cored shouldn't cost more than $200. Stainless steel(non-corrosive) liners will run you about the same. Another thing is you will want to direct vent the outside air for your new furnace anyways. And then remove and cap your pre-existing combustion air well...which is a heat loss.
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