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I'm hoping either an interior or exterior extension will work. I need to get up on the roof and see how he extended it. I'm hoping he didn't cut the new roof jack, if he did I'll have to replace the whole thing.

The interior extension is the only one that will work in your case. The exterior extensions are only for getting the termination higher for snow drifting or problems with air flow over the termination cap from a steep roof pitch due to the furnace's location in the home relative to the peak of the roof.