First, remove front and rear glass, and of course the overhead interior steel trim and upper quarter trim. Remove old headliner, noting which holes the rods were in. Using these is your best starting point later. There should be two wires attaching the rearmost rod to the pinchweld, save them.
You'll need a couple dozen small spring clamps, or a pile of 2" sections of windlace, and some high-quality headliner (contact) cement.
After the headliner has been laid out flat, preferably in the sun, to remove wrinkles and creases, insert the rods exactly as they were in the old headliner. Attach the to rear wires to the headliner rod. Install the headliner assembly in the side rail holes as the old one was installed. Carefully clip the center of the front edge to the pinchweld. This is your last chance to make sure the headliner is OK, so make sure it looks good and will reach the pinchwelds all the way around. Starting in the center front, doing about 6" at a time, using cement only on the top of the pinchweld, cement the headliner across the front pinchweld, using the clamps and/or windlace to hold the headliner. Make sure it's smooth as you go. Now do the same across the rear. Now install the sides, using windlace to hold the headliner in place. It is easier to do this with the roofrail weatherstrip retainer removed, but not essential.
Now install the front and rear glass, using new seals and glass bedding compound, then install the overhead steel interior trim and upper quarter trim.
The coupe is similar, except there is no overhead steel trim, and the seat back and package tray must also be removed.
Now you know why Mustang shops charge $500+ to install a $40 part.
And if anyone tells you he can do it without removing the glass* he's an idiot who will screw up your car, so walk away.
*69-73 does not require removing the windshield, but the rear glass still has to go.
I tried this when I was a teenager (claiming an idiot exemption here). While I could get it to look right without removing the glass, it would not stay.
There are several good threads with write-ups on removing and reinstalling the glass yourself. One includes a neat trick involving string, and several have useful pics.
Are you trying to hook them at the back edge of the pinchweld, where the glass goes? They go at the front edge, the windshield edge of the pinchweld structure.
See the two smaller holes closer to the center than the larger holes?
If they cam ein your old headliner, they'll go back in the new one. Try test-fitting the bow only, then attach the two wires. When I did that, the rear bow wanted to lean way forward, making the wires seem too short. But a little light pressure rotated the bow back into position so the wires could attach as they need to.