How do I reset the sunroof after a new alternator install

Just out of curiosity, is it the motor that is faulty or one of the guides has broken? what are the symptoms you are experiencing?
IF you have a diagnosis and it is in fact the motor, here's how you replace it.
1. Fully close the sunroof glass, disconnect batt negative.
2. Remove Roof trim
3. disconnect Motor harness
4. Remove sunroof motor mounting screw and nut.
After installing the new motor you have to reset the sunroof motor.

A tip to help diagnose if you are just guessing for inop motor
(1) Check fuse for blow-out.
(2) Check switch for improper function.
(3) Check motor for incorrect terminal voltage.
(4) Check relay for improper operation.
(5) Check poor grounding system.
(6) Check harness for open or short and terminals for poor connections.
(7) Check limit switch for improper operation.

Has it always done this? Did you buy new?
Sense I do not know that it's most likely a sensor or control module for the sunroof that has failed to stop it in the vent position. You will likely need to take to a shop that specializes in Sunroof install & repair.

put key in drivers door and hold over (unlock) for 30 secs, windows go down, then open sunroof fully.then put key in drivers door and hold over(lock) for 30 secs windows will go up and sunroof will close,you have just reset the system.....if sunroof rollsback again then the park switch is faulty.

Check for any obstruction in the rail.

Also, can check this procedure to test your components...
Power Sunroof - REMOVAL & INSTALLATION (click over pic for zoom)

Motor
See Figure 1

1. Remove the sunroof switch panel by pushing it to the side and disengaging the pawl, then pulling it downward.

Fig. 1: The sunroof switch panel is retained by a metal clip

1. Remove the sunroof switch bracket.
2. Unplug the sunroof motor wiring harness connectors.
3. Remove the sunroof motor mounting screws.
   

Disassembly of the sunroof motor is not recommended.

To install:

1. Lightly lubricate the drive gear with grease and install the sunroof motor to the sunroof assembly.
2. Plug in the electrical harness connectors to the sunroof motor.
3. Operate the sunroof to verify proper operation.
4. Install the sunroof switch bracket and the sunroof switch panel.
   

Sunroof
See Figures 2 and 3



Fig. 2: Exploded view of the sunroof assembly on 1993-94 vehicles



Fig. 3: Exploded view of the sunroof assembly on 1995-97 vehicles-1998 models similar

1. Tilt up the sunroof lid.
2. Remove the lid side trim.
3. Remove the lid bolts and the lid assembly.
4. Remove the rear drain mount screws and the drain.
5. Remove the shade assembly holders from the sunroof frame.
6. Remove the shade assembly.
7. Remove the sunroof switch, interior accessories and headliner.
8. Remove the switch bracket.
9. Remove the motor assembly, spacer and clip.
10. Remove the wind deflector mount holders from the sunroof frame.
11. Remove the wind deflector.
12. Disconnect the drain hose.
13. Remove the sunroof brackets.
14. Remove the sunroof frame assembly.
15. Remove the link and wire assemblies.
    

To install:

1. Tilt up the sunroof lid.
2. Install the link and wire assemblies.
3. Install the sunroof frame assembly.
4. Install the sunroof brackets.
5. Connect the drain hose.
6. Install the wind deflector.
7. Install the wind deflector mount holders on the sunroof frame.
8. Install the motor assembly, spacer and clip.
9. Install the switch bracket.
10. Install the sunroof switch, interior accessories and headliner.
11. Install the shade assembly.
12. Install the shade assembly holders on the sunroof frame.
13. Install the rear drain mount screws and the drain.
14. Install the lid bolts and the lid assembly.
15. Install the lid side trim.

Hope helps (remember rated this help).

THE ELECTRIC DRIVE SYSTEM FOR POWER SUNROOF IS NOT ADJUSTABLE.DONT REMOVE THE SUNROOF MOTOR UNLESS THE SUNROOF IS COMPLETELY CLOSED.OTHERWISE A NEW MOTOR WILL HAVE TO BE INSTALLED AND TIMED WITH A TOOL THAT COMES WITH THE NEW MOTOR.THE GLASS PANEL CAN BE ADJUSTED.OPEN THE INTERIOR SUNSHADE ALL THE WAY BACK AND OPERATE THE SUNROOF UNTIL FULLY CLOSED.THERE ARE THREE GLASS MOUNTING SCREWS ON EACH SIDE OF THE SUNROOF OPENING.INSIDE THE VECHICLE LOOSEN THE SCREWS SET THE FRONT EDGE OF THE GLASS TO BE JUST 1MM BELOW THE SURFACE OF THE ROOF.ADJUST THE GLASS AT THE REAR EDGE TO BE JUST ABOVE 1MM THE ROOF AT THE REAR TIGHTEN THE SCREWS.

The fuse and relay box on the E30 and E36 models is located in the engine compartment. The E36 models also has relay boxes located under the left side of the dashboard.

Circuit Breakers
Resetting & Replacement
Circuit breakers are located inside the fuse panel. They are automatically reset when the problem corrects itself, is repaired, or the circuit cools down to allow operation again.

One of the less known about fuses that can cause all this to go out is the fuseable link. It is in a black plastic box near the battery. It is an appx 60A thin metal strip fuse. Check the website link to the right for more info.

Also, I suggest check your Fuse Diagram in the BMW 525i Owners Manual here.

Power Sunroof
Emergency Closure Operation
The sunroof is equipped with an emergency closure feature should the sunroof motor fail or the vehicle has lost electrical power. To close the sunroof under these conditions:

1. Remove the front headliner trim panel.
2. Using the 6mm hex key that is included with the tool kit, insert the key into the hex socket and turn the socket to close the sunroof.

Fig. Remove the trim panel to access the sunroof motor



Fig. Insert the 6mm hex tool from the tool kit and turn the hex socket to close the sunroof


Removal & Installation
E30 Models



Fig. Sunroof components-E30 3 Series shown, E36 similar




Fig. Sunroof lid retainer clip location-E30 3 Series shown, E36 similar

1. Open the sunroof lid 2-4 inches (5-10cm).
2. Unclip the roof liner frame and push back into the opening.
3. Close the sunroof lid and loosen the screws on each end of the gates.
4. Pull in the retainers, remove the center screws and lift off the lid.
5. Remove the cover over the motor and gearbox. Close the sunroof lid, if not already closed.
6. Disconnect the wiring harness and remove the 3 mounting screws. Remove the motor and gearbox.
7. Push the cables back evenly on both sides. Remove the rail covers and pull the cables out of the guides.
8. Place the cable in the center position of the gate and press off.

To install:

1. Install the cables to the gate. The cable are marked with the proper side of installation. Do not lubricate fabric covered cables.
2. Pull the cables through guides and align the cables. Insert a hex key through the gate and cable at the 0 position.
3. Install the motor and gearbox. The motor and gearbox must be synchronized with the hole in the drivegear aligned between the centers of the 2 gears. Torque the bolts to 2.0 ft. lbs. (2.8 Nm).
4. Install the sunroof lid. Use new screws and torque to 2.5 ft. lbs. (3.5 Nm).
5. Adjust the sunroof lid. Pull the roof liner frame into position and clip into place.

E36 Models

1. Close the sunroof fully. With a quick actuation of the sunroof opening button, open the sunroof so the back edge of the lid depresses 0.08-0.12 inches (2-3mm).
2. Slowly push the roof liner panel back into the roof. Do not force or use a quick motion or damage could occur.
3. Remove the mounting screws and pull the lid off at the rear side. Do not operate the sunroof with the panel removed.

To install:

1. Install the lid and check that the hooks and levers align. Install the screws with threadlocker or use new micro-encapsulated screws. Torque to 2.5 ft. lbs. (3.5 Nm).
2. Adjust the sunroof lid. Lower the rear of the lid by operating the motor. Pull the liner forward and clip into place.

Good luck.

You must reset the codes that sync these systems and allow them to work read the followning post.

no you should not have to take the head liner out.. when the sunroof is open you should see 3 or 4 screws one both sides.. all you have to do is remove the screws but its better to have a second person so they can hold the glass while your removing the screws so you don't drop the glass..then just put on some cloth gloves(prefered) to hold up and install the new glass. do removal in reverse to install.

Very possibly damaged the alternator; these have six diodes that rectify the ac produced by the alternator (hence its name) and are oriented to produce a positive output/negative ground.  This means that they will conduct if their output has a relative negative voltage applied to the positive output terminal.
If you haven't done it already, you need to disconnect the battery cable or the shorted diodes will drain it completely again and could even damage the plates from heat. 
Generally, rebuilt alternators are quite reliable so replacing with new isn't really justifiable; the commutators and windings are not stressed hard so replacing brushes and diodes and a good (chemical) bath are about all they need to do to restore them. You may even have a local shop that will restore your own unit if you wish.    

Hi Beemer Lover!

I too love the Beems, have had 1600's, 2002's, a 2002tii(!!!), 320's, and even had a gray market 635 (WOW!).

I believe the sunroof crank attaches like the window cranks... that is there is an outside covering over a metal crank arm that can be pulled away from the metal exposing a hole where an attachment screw fits through it into the sunroof crank splined shaft center.

Hope this helps, and good luck!

-WB