Any chance it's the AC amplifier? I'd like to make sure it's the blower controller before buying a blower assembly.
Logical trouble shooting, I love it.
My theory is that the electronics inside the blower assembly act like a simple Triac controlled lamp dimmer, or speed controller. By varying the voltage on the gate (or more specifically the time that the gate is opened) we control the voltage getting to the device.
In this case it looks like the varying gate voltage is the SI signal from the amplifier, and the power for the motor comes on the B+ lead. Which may just stand for battery, or many older engineers still make reference to the B+ plate voltage used on vacuum tubes.
So you know that you have full battery voltage on the B+ line (Pin #3), and I assume you checked for a good ground on Pin #1, so you only need to see if the duty cycle of the 1v square wave on the SI line (pin #2) changes as you adjust the fan speed.
If you have a scope, then that's the way to go. Otherwise try using an old analog voltmeter ( with a mechanical meter and pointer)
on the DC scale. Analog meters have the magic ability of displaying the "average" value of a varying DC voltage. When the duty cycle is near 1% on- 99% off, the meter will read near zero. at a 50-50 duty cycle the meter should read ~.5 volts, and at a 99-1 duty cycle it should read ~1v. Be aware though that depending on the meter, it may be difficult seeing a voltage this low.
Am going to jump connect the motor directly to connector E-53 and make sure we're good there. I did measure 13.3 vdc so no reason that shouldn't spin the blower motor too.
I assume you want to do this test to determine if the B+ pin on E-53 can deliver the proper current. As long as you're using jumper leads from the motor to the B+ lead, and not plugging E-53 onto the assembly it should be OK. I think if you were to short out the internal circuitry with E-53 connected then you could risk damaging the amplifier via the SI lead (Pin #2).
Or am I over analyzing, just buy a blower assembly from the junkyard?
You don't seem to be having any problem following the diagnostic procedures, so why not continue and make sure you are replacing the proper item.
EDIT: The location of the AC amplifier is shown on page AC-7 of the manual.