Yes, you should see 12V+ on both sides on the light blue/black wire at the switches. Even if the switches have voltage, it needs ground, too. Power window ground (G101) is a single black wire bolted to radiator support, on the engine side, at the upper driver side of the radiator opening. Look for a black wire with a ring terminal coming out of the harness going across, and make sure it's bolted tight to clean metal. The motor wires should both show ground, except when either switch is operated. It's easier to troubleshoot the driver side first, then the passenger side.
Sounds like you're making progress. Did you get the motor to crank and run?