The back glass has to go in before any of the interior trim, because the trim abuts the glass gasket.  The way the fastback interior trim is installed you start with the rearmost lower panels first and finish with the two metal panels across the roof.  It all goes in a specific order.

Having done exactly what you're doing already I would advise that if the car's been apart and put back together multiple times (you can tell if there are for example multiple holes to mount the trim in the mounting brackets indicating its been moved around and new holes drilled over the years) you weld all the holes shut and drill new holes at the time of installation.  Typically you will take more time than even the factory did and get the alignment better.  You will likely need shims to accomplish this as well. 

If you are replacing the headliner you can actually do it either way depending on how good you are.  IMO its preferable to have the glass out when replacing the headliner.  There are people who will leave a flap of the original material about 1.5"long around the glass, and then carefully glue and tuck the headliner to that flap and under the gasket respectively. 

Only dumb question is the one not asked! I have a 67 fastback and have done this many times. Yes, the glass should be in before interior reassembly. The real job is sealing that huge back window. Do you have any experience with window install? Do not use urethane, you must use 3m8509 glazing compound or something similar, it must stay flexible. You cant use enough of this stuff. If you knew this already, i apologize for repeating. I also put a few extra trim clips on each side and in the corners. There is a great you tube video from Mustangs to Fear on a 67-68 windshield install that explains everything. This is the way the factory installed them. He uses the eurothene at the very end but not eas the main sealer. And you dont have to take out your windows to install a headliner.  It can get messy, but better messy than having a leak!

rtmjr13@optonline.net wrote:

Only dumb question is the one not asked! I have a 67 fastback and have done this many times. Yes, the glass should be in before interior reassembly. The real job is sealing that huge back window. Do you have any experience with window install? Do not use urethane, you must use 3m8509 glazing compound or something similar, it must stay flexible. You cant use enough of this stuff. If you knew this already, i apologize for repeating. I also put a few extra trim clips on each side and in the corners. There is a great you tube video from Mustangs to Fear on a 67-68 windshield install that explains everything. This is the way the factory installed them. He uses the eurothene at the very end but not eas the main sealer. And you dont have to take out your windows to install a headliner. It can get messy, but better messy than having a leak!

I removed and reset my rear glass by myself when I was about 17.  The trick was running weedwacker line inside the channel in the gasket that rolls over the body.  Leave two tails and drop those into the interior.  It is then quite easy to use the line to work the gasket over the glass channel around the opening.  I also put some weatherstrip adhesive inside that channel on the side where thew gasket meets the metal on the outside of the opening.  Hasn't leaked in over 20 years.  Maybe its better to be lucky than good, but all I know is it worked.