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Trouble-shooting that heater controller without a schematic of its innards seems like a crap-shoot, IMO... One thing you CAN do is try to isolate whether it's the cause of the bizarre blower motor behavior. To do that, I would use a volt meter to observe the voltage at the motor [at its connector]. If the voltage fluctuates coincident with the motor speed, then you can go to the uncovered controller and check the voltage at the input and output of the relay. You can also observe the relay in operation to see if it's moving or is solidly picked.
It's interesting to note that the blower motor's ground is on the #1 intake runner, but it gets there via a connection on the back of the alternator [according to the Bentley schematics]. This should be kept in mind if you find voltage variations across the leads at the blower motor.
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