Whenever the "Check Engine" light comes on, there is always a DTC (Diagnostic Trouble Code) stored in the ECM (Engine Control Module). You'll need an OBDII (On-Board-Diagnostics) scanner to retrieve any codes recorded/set in ECM. Research of the wiring diagrams indicate there is no relationship/connection between the Check Engine light (Engine Management System - EMS) and the Power Windows circuit. Check all your fuses (Passenger compartment) fuses 16 & 20 & fusible link (30 amp) supply power to the power windows (as well as to Stop lamp switch(cruise), head lamp, A/C relay.
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