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... When the heater is first turned on, the blower starts. After the furnace heats up for 3 - 5 minutes the noise starts. When the flame turns off(blower still on) the noise goes away.
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It sounds like something in the sheet metal is expanding as it heats up, to the point where the blower fan hits it. If you disassemble the sheet metal blower-motor area, you ought to be able to see scrape marks. Bend the sheet metal a bit, or tweak the blower position a bit. You shouldn't have to increase the clearance very much to stop the problem.
Let us know the result.
Bill