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Sounds like you already suspect the heater core. The original cores I've seen are divided in half with separate outlet pipes joined in the center. So if you feel cold air from one vent and warm air from another, at the same relative strength, this division in the core is the only plausible influence.
You didn't have that symptom before you did the replacement, so it is just likely the surgeon dislodged a chunk of plaque into the constricted arteries of the heat exchanger and your core had a "stroke".
Before doing a transplant, try confirming the diagnosis by going in through the upper radio slot or center vents (maybe arthroscopically from behind the glove box?) to feel the copper exit pipes on either side of the top of the core before they join in the center. Then arrange some configuration of garden hose and maybe heater hose and a five gallon bucket to reverse flush the core.
Actually, I just read an excellent thread on salvaging the heater core suggesting a chemical cleaning method.
I'm waiting for the snow to subside to replace a heater core, so if you're not lucky with the backflush, stay tuned for anecdotes on a core transplant.
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Art Benstein near Baltimore
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