Pontiac exhaust manifolds, including the log-style and high-performance ones, such as the Ram Air III or long-branch, generally have excellent port matches from the factory.
Custom headers generally have 3/8- or 1/2-inch header-flange thickness and are CNC machined from 1018 cold rolled steel or 304 stainless steel. If you are having custom headers manufactured, ask the manufacturer about the flange construction and provide them with a cylinder-head exhaust template, so it is clear from the outset that you want perfect head-to-header port alignment.
Stainless-steel flanges and headers can be repaired using the same procedures outlined in the article. However, stainless brazing and welding is best left to a professional, as it takes years to acquire the skills to successfully perform the repairs.
Conclusion
According to Steve DuSold, "Even the most expensive production headers can have mismatch problems with the cylinder head. I commonly see better port alignment on the premium headers, but not always.

Next, the template is removed...

Next, the template is removed and turned over to examine the impression marks and ensure that they are visible.

A fine marker is employed...

A fine marker is employed to carefully trace around the exhaust ports.

Once done, a razor blade cuts...

Once done, a razor blade cuts out the traced areas. (Take your time and have several new razor blades at the ready, as they will wear quickly and you do not want to tear the paper.) Precision in tracing and cutting can't be emphasized enough, as the template will dictate what work will be performed on the exhaust header(s).
"In addition to port alignment, you have to make sure that the header flange is level. Mild deviations in port alignment and flange straightness are to be expected, but major problems are time-consuming and expensive to correct. As the number of issues that a header has with port-alignment grows, so too does the adverse effect on performance. Perfectly aligned headers may only pick up 5-10 hp over non-aligned headers, but a set of headers with issues like those demonstrated could cost you 20-30 hp.
"If you blow out header gaskets on a regular basis, it usually isn't the fault of the gasket or installation, but rather a poorly aligned header tube."
All headers are not created equal, so if you have port-alignment issues and the repair is anything more than a few quick minutes with a grinder, make a determination as to whether or not the headers are worth fixing and you have the resources and skill level necessary to get the job done. If the headers are worth keeping, DuSold Enterprises can perform the necessary repairs and charges are based on the time required to do it. Estimates are given over the phone, and once the header(s) and template are shipped in, a firm quote is provided.
If you are in the market for headers, research the available offerings carefully and have a cylinder-head template prepared to bolt up to the header as soon as the box arrives. If the ports aren't aligned to your satisfaction, contact the manufacturer and return the headers. If a second set from the same manufacturer has the same problems, either switch brands or determine if it is cost-effective to fix the headers, over having a custom set manufactured.
Pontiac headers are notoriously difficult to install, especially on well-equipped street cars, so it would be a shame to go through the time, money, and effort to install them, only to end up with no gains in performance. If you already have headers installed and want to maximize their efficiency, create a template and see how they align. You might be pleasantly surprised or "red-faced" angry, but the only way to know for sure is to give it a try.

With the ports cut out, the...

With the ports cut out, the template is turned over and examined, and then matched up with the head ports again to ensure that there are no tracing or cutting errors.

The template is then bolted...

The template is then bolted to the header with two bolts and each port is carefully examined to determine if there is proper header-to-port alignment. Ultimately, the header ports must be slightly bigger than the port opening in the head. In this case, there was an excellent port match, as the header was not protruding into the exhaust-port openings and the tubes were just slightly larger than the cylinder-head port openings.

Since no repair work was necessary...

Since no repair work was necessary on the passenger header, a "budget" mid-length set of headers for the same application was donated to determine if either of the two headers would require repair. After putting the template up against both headers, the driver-side header was excellent for illustration purposes, as every port would require modification! Note how the header flange is visible through each port opening.

The worst mismatch is on the...

The worst mismatch is on the front header tube. Note the large amount of header material visible through the template, and the header tube is 0.226-inch from the left edge of the template. This tube will require two repairs, one to remove the excess material in the port and a second where the tube is brazed to add material so that there is proper port alignment.

The first procedure will be...

The first procedure will be to remove the excess material, so a marking pen is used to scribe the material hanging into the port opening.

The template is removed, and...

The template is removed, and an air-powered die grinder with a carbide-cutting bit is used to remove the excess material. As it's removed, the cut is blended back so that the exhaust flow can smoothly transition into the header. After removing the material that was scribed, the header template is placed back onto the header and the port alignment is checked. After verifying a port match, Steve examines the outside of the tube to ensure that the grinding operation didn't break though the tube wall. It didn't, so the first repair procedure is complete.