I'm not shure what you mean by "I can't get the motor to engage to the proper distance", but if you mean that the roof does not stop in the right position, it can be adjusted as follows:

Inside the drive unit are two switches, which sense the position of the
roof (or rather the drive cable to the roof). There is a white knob on
the drive unit, which can be pulled out to "adjustment position", in
which it disengages from the drive cable. The drive unit gear can then
be turned by the knob independently from the sunroof. Turn it several turns cw and ccw and listen when the microswitches are actuated. With the sunroof closed, the drive unit shall be aligned just in between the the two switches actuating. Then push in the white knob, and see if it the sunroof closes correctly after having been opened or lifted. Readjust if necessary.

If it doesn't work this way, the microswitches may be bad, or there may be a bad connection in the wiring/connectors.

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1991 300SEL (W140)
1987 190E 2.3 (W201)
1987 Honda Accord 2.0