A person can use the rope method in some cases yours must be one of them. Its been a long time since I've done a 66-67 non lock type. On some of the gaskets the bottom basically lays on the bottom of the cowl so sitting the gasket first is best {for me any way}. If you haven't already removed the new glass why not try and seal up what you have with the urethane between the gasket and glass by having the tip of the tube cut very small and inject the sealer back as far as you can under the seal just take it slow and easy trying not to skip or miss any area. Then use the bedding and glazing product for the area between the body and gasket I've been able to apply this from the side of the car as well but the bottom really needs to be sealed before the glass and gasket is set in the body. You may be able to inject this under as well. Give it a try, what do you have to loose but a little time.
I always wear hand protection {nitrate gloves} when working with the urethane it's something you really don't want to get on yourself and don't be wearing your favorite T shirt! once this stuff gets on your cloths its on for ever!
Another thing that really help when working with the sealer is to heat the tubes up and not use them when below 70 degrees. I use my heat gun about a foot way from the tube until they are nice and warm