We salute the venerable '79-'04 Fox-body Mustang for its huge contribution to the history of America's favorite fun car. With 25 years of evolution and improvement, there are plenty of them out there to restore, build, and enjoy.
Fox-body Mustang restoration today is much like it was 25-30 years ago for those of us with classic '65-'73 Mustangs because finding restoration parts is one of the greatest challenges. Some reproductions are available, depending on the model year, and some parts remain available from Ford. When those two options fail, there's new-old-stock as you can find it on eBay and other sources. Fortunately, the product planners at Scott Drake Enterprises are looking closely at this market to see what they can do for '87-'93 Mustang restorers and builders.
Each quarter window is a glass/rubber-bonded...
Each quarter window is a glass/rubber-bonded assembly, with nine studs that go through the body for fastening from the inside with a nut/washer combo. Rubber contacts the body to provide a leak-tight seal. This is one reason why late-model Mustangs don't suffer from leaks like vintage Mustangs.
The latest Scott Drake reproduction part for Fox-body Mustangs is the E7ZZ-6129710-1B quarter window for '87-'93 hatchbacks. Available from Latemodel Restoration Supply, this is a really nice piece, although purists will notice the absence of the "MUSTANG" graphic in the glass. If you must have the lettering for concours or other purposes, you will have to find NOS or excellent used.
Fox-body Mustangs ushered in a new era of manufacturing technique. Where the classic Mustangs had roll-down quarter windows, '79-'93 Mustangs did not. Removal of the old glass is not easy because it is both studded and sealed into place. And because the bonded areas are difficult to reach, you run the risk of breaking the glass during removal, which is best approached from the inside with careful separation of rubber and body in baby steps with a putty knife. We enlisted The Custom Shop to replace our '87-'93 Mustang hatchback quarter windows. Keep in mind coupe quarter window replacement works the same way though a reproduction is not yet available.

Surface preparation is necessary...

Surface preparation is necessary prior to installation. All contact surfaces must be clean and completely free of old sealer.

Interior quarter trim panels...

Interior quarter trim panels must be removed for access to the fasteners. This process is easier on Fox-bodies than the classics. If your Mustang is fitted with a stereo system, don't forget to disconnect the rear speakers.

The Mustang hatchback body...

The Mustang hatchback body didn't change from '79-'93, even though '87-'93 looks different. Ford's restyling efforts for '87 were bolt-on-fascias, taillights, and broad glass quarter windows that covered the same area as glass and trim for '79-'86.

Before installation begins,...

Before installation begins, surfaces are outlined with masking tape to protect the paint.

There are a couple of choices...

There are a couple of choices when it comes to window sealer. The Custom Shop is using R-900 windshield sealer from ADCO Products, available from most auto body supply stores. R-900 is a permanently flexible sealer that expands and contracts with temperature changes for a leak-proof joint. You can also use 3M Windo-Weld Resealant (No. 08634), which is more like glue and less like a sealant, or 3M Fast 'n Firm sealer (No. 08505). Apply sealer at contact points around the window.

The window assembly is firmly...

The window assembly is firmly pressed into place for the initial set.

The glass shop that removed...

The glass shop that removed our original quarter windows managed to lose the Ford fasteners. Our local Ford dealer did not have the fasteners. A visit to a True Value Hardware store netted the 18 fine-thread metric nuts and flat washers. Ideally, you will use Ford fasteners, which are typically tinnerman's nuts with blended washers.

With a helper pressing on...

With a helper pressing on the glass from the outside, thread each nut until snug.

The Custom Shop discourages...

The Custom Shop discourages the use of a ratchet when tightening these fasteners because overtightening can accidentally break the glass. Tightening should be done in a criss-cross fashion and just snug enough that the window is firmly seated.

Reinstall the quarter trim...

Reinstall the quarter trim panels, taking care not to overtighten the fasteners, a combination of pop-in fasteners and screws.