Shown here is the typical weld-in cowl patch, as seen from under the dash and installed on the passenger side (the heater box inlet butts up against the opening).
The well-travelled vintage Mustang owner knows that the hobby's biggest four-letter curse word is r-u-s-t. Rust has ravaged its fair share of vintage Mustang body panels and one of the more problematic areas is another four-letter word that brings chills to Mustang owner's spines—the cowl.
The '65-'68 Mustang's cowl design is certainly not one of Ford's better ideas. The cowl panel is made up of an upper and lower sheetmetal stamping that is welded together and welded to the firewall as well as the windshield framework. Unlike today's coated metals and robotic painting processes, the cowls in '65-'68 Mustangs were simple sheetmetal parts spot welded together and given a coat of paint, certainly not the most rust preventative measures. Combined with the sealed design, it was a rust issue just waiting to happen.
Starting in 1969, Ford made the cowl area a bit more accessible via a removable grille panel, mainly for servicing the wiper motor and transmission, which also made it easy to keep the lower cowl clean of debris. This debris is what causes the rust issues in the '65-'68 design.
While Ford did design a drainage trough on each side of the cowl that exited the cowl sides into the fender area, the drains easily get clogged with pine needles, tree leaves, dirt, and other debris that enters the cowl vent opening. This debris traps moisture in and against the steel of the lower cowl panel. The combination of air and moisture over time initiates the metal's transformation into rust. As the rust worsens, causing penetration of the cowl panel around the cowl vent's "hat," the ensuing perforation allows future water ingress (natural rains, car wash water, etc.) into the passenger compartment, soaking the carpet and causing further rust issues with the floor pans, the Mustang's next biggest rust issue.
If you're one of the lucky few to have a garage-kept vintage Mustang or perhaps lived in a southern and dry climate, then you most likely have nothing to worry about. However, for the rest of us, cowl vent rust and leaks are a real problem. Some may say that the only proper repair is to cut out the rusty cowl portions and weld in patches or a new cowl. While we agree with this wholeheartedly, we also understand that not everyone has the budget for a complete cowl replacement. Not to mention some cowls may have minimal rust while others look like Swiss cheese. So for a cowl with just a couple of small holes, a complete replacement is a bit of overkill.
Thankfully there are several solutions that vary in price, practicality, and the amount of labor involved. Read on as we go through each solution and the pros and cons of each.
If you suspect you have a cowl leak, a bucket of water or a stream of water from a hose will help diagnose the situation and pinpoint where the leak is coming from. Just don't mistake a leaking windshield gasket for a cowl leak. It is often best to gut the underside of the dash (gauges, wiring, wiper assembly, heater box, etc.) so you can get a clear view of the complete cowl to determine where any issues lay. If your car has a nice paint finish and you don't wish to repaint the cowl and/or pull the windshield, some shops will install the cowl patches from inside the car, but the welding/sealing is more difficult in this manner and, as such, be prepared to pay a little more. Speaking of cost, we've outlined the parts cost and typical labor costs for each option below.

With fenders removed, you...

With fenders removed, you can see the drainage opening in the cowl side panel. This drain was partially blocked with leaves, pine needles, and even bird feathers, plugging the drain and causing cowl area rust.

While we’re going to discuss...

While we’re going to discuss all of the options for cowl leaks, by far the most common is the patch panel. The left and right patches are designed for the ’65-’68 Mustang and are usually large enough to repair any rust issues when welded in as shown here.

Once the cowl patch or lower...

Once the cowl patch or lower panel is welded in place, the original cowl top panel (if usable) is aligned to the cowl and the spot weld holes previously drilled out are used as attachment points via MIG welding. Here the welds have been ground down with a grinder and ready for seam sealing, priming, and paint.

Accessing the inner/lower...

Accessing the inner/lower cowl panel, where rust normally is found, means removing the upper cowl panel, which is spot welded in place from the factory. To find all of the spot welds, you’ll be removing both fenders, the hood, wipers, windshield trim, and the windshield itself. There are several hundred of these spot welds that need to be drilled out to separate the panels.

Once the upper cowl panel...

Once the upper cowl panel is separated, you’ll have gained access to the lower cowl panel and the two cowl vents that feed air to your driver’s side vent control and the heater box. These low lying areas are where wet leaves and other debris back up and create the rust-through issue.

As mentioned in our opening...

As mentioned in our opening text, the cowl assembly is an integral part of the Mustang’s unibody structure. If complete removal of the lower cowl panel is necessary for repair, you would be wise to support the car properly and tack weld in some bracing, as has been done to this K-code coupe under repair, to prevent tweaking the unibody.