Doug, I took the plunge a number of years ago and did my own replacement on a '68 coupe that I owned. A p.o. had done a replacement with a homemade vinyl top....yikes!! Needless to say, a quality repop vinyl top went back on.
The lower pillar moldings were there, but the drip rail inserts were gone. I was able to find a set, but it took awhile AND they were actually off of a '66 coupe. Be aware, the rivet locations are different if you consider this. I ended up filling the drip rail holes and re-drilling to match the '66 holes. Afterward I found out that most professional top installers don't both with re-installing them. Obviously, if you want Concours, this would be an issue.
As others have stated, the top does get tucked under the front and rear glass. If you want to do it yourself, here's a couple of tips:
-Make sure your sheet metal is smooth and flat after your repairs for rust. The vinyl will NOT hide dents,depressions or other deformities. Look at the sheet metal as if you were applying paint.
-Do it on a warm day. Let the top lay out and warm and "relax" in the sun prior to starting.
- Don't use any brush on adhesives, stick with high quality spray. Brushing can allow little "wads" to collect as the glue is being brushed. You WILL see them under the vinyl.
-Measure your vinyl top from seam to seam and find the true center of it at the front and rear. Mark those locations with chalk (on the top surface). Do the same to the front and rear window openings. You can make those marks with a marker or paint pen.
-Apply a narrow line of adhesive down the centerline of the roof and vinyl. Line up you center marks of the roof and top and set this in place first. Your top should be perfectly centered now. Just don't pull too hard to either side as you initially start laying the rest of the vinyl down.
-Do only one half at a time (i.e. the driver's side of the roof). Work from the center outward laying the vinyl down.
-DON'T lift the vinyl up to reposition for small errors. They can generally be smoothed out, if you were being careful to start with. If you lift the vinyl back up, you will get lumps!
-Be extra careful on the pillars. Though they are relatively flat and vertical, they can get tricky if you get too relaxed (you should be nearing the finish line by the time you get to the pillars).
-A second set of hands is VERY nice to have around, though not absolutely necessary.
-Take your time and don't be intimidated by it or feel rushed.
-Make sure the vinyl is tucked into all the nooks and crannies BEFORE final trimming.
Finally, step back and enjoy your hard work!! Actually, it's not really hard, just a little tedious. It's and instant gratification feeling though when you done!! Good luck!!
John
The hardest part was putting the windows and trim back in with enough sealer and then the trim. You need to be real careful with the trim, one slip and you could rip the new top...yeah, yeah I did it 
