Does this system use a plug and socket anywhere? Meaning in the power or control circuit? A plug and socket means fast connection and two points either side of the plug as well as within the interface itself. Because the control circuit was replaced that would eliminate that section. Does the motor power wire bolt on, or is it a in the form of a socket and plug? This may well be a control issue from where a controller meets a harness - 
The pro-way to diagnose this is to find out the power circuit amperage draw. Substitute a 50 or 100 watt 12-volt light bulb for a synthetic load. Try the power circuit. No light, there is an open in the power circuit. Then do the same thing with the control circuit using the "correct" 12-volt light bulb as a synthetic load.
Diagnosing a power circuit failure by a static resistance reading requires a 4-wire milli-ohm kelvin bridge meter. This is the difficult way to do things.
A 100 watt 12-volt light bulb is CHEAP at a NAPA auto parts store. The screw-in light bulb base is a hardware store item as are two wire alligator clips.
Even a SLIGHTLY DIM bulb means trouble. Compare it to what you see connected across a battery as a test.
I prefer diagnosing problems like this the easy way. Few mechanics are savvy enough to use a synthetic load test. At $100/hr sometimes I wonder...