I recently replaced the alternator and while working under the car, my daughter pulled a jumper wire from the fuse box. I have no idea where it goes and neither does she (isn’t she sweet). Is there a chance this sent power to the 2 fuses that control the power windows? They all don’t work now that the car is up and running.

Maybe post a picture of the jumper. Have you checked for voltage at either end of those two fuses (a and b)?

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1998 C230 330,000 miles (currently dead of second failed EIS, yours will fail too, turning you into the dealer's personal human cash machine)
1988 F150 144,000 miles (leaks all the colors of the rainbow)
Previous stars: 1981 Brava 210,000 miles, 1978 128 150,000 miles, 1977 B200 Van 175,000 miles, 1972 Vega (great, if rusty, car), 1972 Celica, 1986.5 Supra

I plan on checking the voltage tomorrow. The jumper is completely off and mia. It was just a wire with alligator clips. I’m thinking it was bypassing fuse 2 to the power window relay and jumping over to a/b.

Yep, jumper went from fuse #2 to b bypassing the relay. Thanks for the response.