Don't fool around physically with the microswitches - that is to say, alter their position relative to the cam. They are set at the factory to ensure the motor rotation stops before the sliders encounter the physical end of the guide rod. If you upset that adjustment, you are in for a world of pain getting it right again (much like altering the butterfly linkage screws on a throttlebody assembly).
The electrical operation is really straight forward (at least for me it is).

The circuit has two logical parts -- the lift/lower relay control logic and the motor control logic.
First the lift/lower relay control logic description. Battery power is fed to the center of the Window adjust switch (L/Y) and each side of that switch goes to one side of the coil of each relay. The other side of the relay coil goes to ground through a given microswitch. Let's say the operator presses the window adjust switch for UP motion. Current will flow through the switch to the lift realy coil, through the Up (micro)switch to ground. The lift realy coil is energized and the windshield moves (we'll get to that description in a minute). When the cam on the motor encounters the limit, the Up microswitch opens, breaking the circuit and the relay coil de-energizes and the motor stops. The exact same operation happens if the Window adjust switch is pressed for DOWN motion. A consequence of the cam design is that at no time are both microswitches open -- there are always at least one switch closed, making contact.
Second the motor control logic. Battery power is wired to the N/O (pin 87) of each relay through the R/L wire and ground is wired to the N/C (pin 87A) of each relay through the Br wire. The common contact (pin 30) on each relay is wired to one or the other side of the motor (Gr and L wires). In a rest state, each side of the motor is grounded and remains so unless the button is pressed. Let's say the operator pushes the Window Adjust switch for UP motion -- the Lift relay energizes and the relay contact switches battery power to the Gr wire. The power travels through the motor windings through the Lower relay to ground. The motor rotates. When the button is released or the micro switch limit encountered, power is cut to the relay, the contacts drop and power is cut to the motor. Now, if the operator presses the Window Adjust switch for DOWN motion, the Lower relay is energized and power travels through the L wire, through the lift relay to ground. the motor reverses direction because the direction of the current flow is reversed. The windshield lowers until the switch is released or the limit encountered.
This description will help to debug wiring problems. For example, to bench test the windshield, apply power directly to the motor in different polarities to see that the motor is functional. Understanding the operation will lead you to understand that at no time can both switches be open; only one is open at any one time when a limit is encountered or both are closed during travel.