Getting the glass to seal properly as has been discussed is a major job for even the experienced restoration shop. On the very same car, you can spend 2 hours and have everything fitting very nicely. Move to the other side and do everything the same way and spend six hours and it still does not fit well.
First off, I strongly suggest trying to find good used door and roof rail seals. We have been involved in manufacturing / selling weatherstripping for 28 years now and have seen and heard most of the horror stories. Depending upon the year model and body style makes a huge difference in which brand to purchase. If your doing a 66 to 67 B-Body, the only roof rail seal that will seal remotely is the Steele Rubber piece. For the 68 to 70 B-Bodies, Soft Seal and Metro are the two most widely used pieces. I am hearing all kinds of issues with people using the OER brand of seals. The thing about any seal is that rubber is very inconsistent from production run to run. Even with current technology, cooling time, pressure variations and mix variations will make a difference in durometer readings and thus one set from vendor X works very well and on the next order, your not able to close the doors without slamming them.
As Justin pointed out in his pictures, make sure that the roof rail is seated properly into the stainless channel. Cocked the least bit and the glass does not fit into the relief. The factory seals have a pronounced rib to aid in installing them. Metro has a tendency to have a bulb size that is slightly oversized holding the glass off. Soft Seal on the other hand is more profile correct, but they have issues maintaining the durometer value which impacts the ability of the glass to seat itself into the relief.
I strongly suggest the service manual to be read and scrutinized when starting to install the glass on any car. There are much more adjustments that most people are not willing to play with to get them to fit right. The best thing I have learned when things are fighting you, take a break from the procedure and come back the next day with an open mind. Take a big swing with the adjustment and see where it takes you and start to dial it in from the two extremes.