Done! I finished this a couple weekends ago, but I am just now getting around to posting the results. It took a lot of time to sew the window in by hand (4-5 hours total), and I could definitely do better on a second run, but it looks pretty good. I was able to sew it in using the previous thread holes. Also, using the basting tape seems to have made it water tight even without re-sealing the top, which I need to do anyway.
Step 1: Remove top and frame from car
Step 2: Trace the shape of the existing window to a piece of paper while the top is open, but not under tension so the vinyl is not stretched to the closed position (no pic). I used the piece of paper that came with the new vinyl to keep it from sticking to itself. I put the piece of paper over the window, pressed the hem with my finger all the way around the window to transfer the indentation, then went over it with pencil to make it visible.
Step 3: Seam-rip the window out (no pic). Be careful not to damage the canvas, scratching the old window is of no consequence, so concentrate your force toward it. There's only one row of stitching, and some glue, holding the window to the canvas. There's also an inner trim piece of black vinyl. I reused this piece. I simply used the basting tape to stick it onto the new vinyl piece.
Step 4: Trace the outside of the removed window to the paper used earlier. This'll give you a template that has the hem line and the final outside shape of the vinyl.
Step 5: place the new vinyl over the template and trace the hem line and the final outside shape on it with a fine tip sharpie.
Step 6: Trim the vinyl to a manageable size, but DO NOT cut it to the final size line. You'll want enough material left that you can pull on it while sewing. I put a single layer of basting tape to the outside of the hem line all the way around. I also added several rows of basting tape on the extra margin of the vinyl to help hold the window in place while sewing (this turned out to be of little help)
Step 7: Set the top up and prop it open. I used the bed in our spare bedroom. The top went on the bed, the back went on the floor and rested on the frame. This was pretty ideal since I could flip up the back freely (as if accessing the engine) to have easy access to the inside and outside for sewing. The pic is before sliding the vinyl into the inside of the top. I failed to take any pictures during the sewing process, sorry.
Sewing Notes: Half way through sewing, after wrestling with the basting tape on the vinyl coming unstuck repeatedly, I figured out to use push-pins poked through the existing thread holes, through the vinyl, and into wine corks as clamps all the way around the window to hold the vinyl in the final position. This made the remainder of the sewing MUCH easier and made it easy to lay out the position of the window to the hem line and preemptively take out any wrinkles. The other thing that helped a great deal was a heat gun to soften the vinyl a little.
Step 8: Enjoy the new window, and save a bunch of money that doesn't have to come out of the IMSB/clutch/RMS/water pump 65k maintenance pot.
