The insertion of the pin is easier if you do the below, I'm trying to follow that part of your DIY, but you lost me at inserting the large pin when the regulator and window are in the same place. You remove the panel and expose the glass. The glass should be pulled all the way up. You insert the larger dowel into the window hole, slit down. Then you insert the small dowel into the larger with slit up. Now reinstall regulator panel. Then take window glass and push it into the regulator. The regulator has two ramps that allow the pin to go into place. If it doesn't fully go into the hole, then just move it with a screwdriver to do so.

Not raining on your parade, this is an excellent write up, however, the factory method is the most time efficient and correct.

http://www.passatworld.com/forums/68-b5-garage/352833-correct-way-replace-rear-window-dowels.html

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Thank you for the info..im sure others will find this helpful...i ultimately ended up replacing the whole pin with a little nut/bolt action to avoid the pin popping out for a third time.