I'm in the process of doing this on my '87 targa. To answer your question, remove the triangle window and frame with the door window in the down position.
I am using what are most likely "Middie" ventilator windows/frames. Originally they were black from the factory and are brass. After a complete refurbish and attempted install, I have noticed that these frames are slightly thinner than the factory fitted triangle window frames on my 1987 MY targa. No issues with the door window and channel, but I am having to "engineer" the seal/joint rubber at the leading edge of the door where the ventilator frame meets with the door.
I have concluded there was a change in frame width starting in 1987. According to the PET, the 911 531 711 41 01C Joint Rubber left and the 911 531 712 41 01C Joint Rubber right are required on my model year and newer targas and since ventilators were not an option on late MY targas, the two new joint rubbers that I have to install are wider to accommodate the wider frame of the '87 and up model year targas.
The joint rubber is the small piece of plastic secured by a plastic rivet at the bottom of the leading edge of the triangle window. On my factory triangle window, this piece fits snugly around the double contour of the inner portion of the frame. The same is true for the new joint rubber I have to install. The new joint rubber is correctly sized for it's application and unfortunately needs to be adapted to the thinner ventilator window frames.
Furthermore, addressed in the factory service training center bulletin on Sealing of 911 (a PDF I can send if you would like) is the proper installation of the joint rubber onto the window frame where Porsche recommends drilling into the triangle window frame to allow for the retaining plug to securely fasten the joint rubber. Apparently the door/windshield frame to window seal prior to '87 was molded with a transition piece which didn't require the joint rubber part.
Be aware of potential wind/noise/water intrusion if this joint rubber/transition isn't properly addressed. My plan is to place some foam/rubber and butyl tape on the inside of the window frame so as to ensure a proper seal to the door/windshield frame seal. It will probably require more butyl tape (what I refer to as gum-puckey) than I would like. We'll see how it turns out.
