I have owned vans for 25 years. Right now I have a 2006 Ford E-350 Super Duty with the 5.4-liter motor and 4 wheel disc brakes. I use it as a personal/work truck. While pickups have been lavished and glorified with everything from sport packages to luxury treatments, the van has been one of the best selling but neglected vehicles in history.
I cannot find anything from computer chips to exhaust systems for my application. I cannot even find better stopping brake pads front and rear! I was wondering if this van shares anything with the pickup trucks, I know in the past, there used to be interchangeable parts manuals for cars (I used one in the early 80s, the motor mounts for a 74 cougar with a 460 V8 were a bolt in for a 77'-79' Thunderbird/Cougar because they had the same exact frame. I dropped in a 460 with the matching dual exhaust, it was awesome).
It can be tough finding performance parts for a van. They're typically work trucks since the custom lava-lamp trims faded out. But the E-350 Super Duty van is the same basic platform (frame, suspension, drivetrain) as an equivalent 1-ton Super Duty pickup. Not all, but some stuff will be interchangeable.
I did a little poking around and discovered that Hypertech produces electronic power-tuning products for a 2006 E-350 with a V10 gas or 6.0-liter Power Stroke diesel engine, unfortunately, nothing for your 5.4-liter V8. And Hypertech does not recommend using their products for anything but what they are listed for (even a common platform/drivetrain) due to the specific calibrations involved.
Borla exhaust has a listing for a throaty stainless steel exhaust system for an F-350 Super Duty with the 5.4-liter, but not for the E-350 van. Borla tech support suggests welding in their universal muffler to your stock pipes.
If you have time to spare, when dealing with an exhaust and certain other parts, you can speak with Ford parts and compare part numbers. Let's say an '06 F-350 Super Duty pickup, with the same drivetrain and wheelbase as your E-series, both share the same exact Ford part numbers on both exhaust systems. I can't guarantee it, but it would be reasonable to assume that the Borla stainless steel exhaust for that F-350 would also fit the E-350.
Double check with a phone call, but EBC brakes does show listings for performance brake pads for your specific Ford van. Personally, I'm a satisfied customer stopping on EBC pads and rotors on my sport-touring motorcycle.
As far as the parts swapping you did on your Ford/Mercury classics, the Hollander Interchange Manual most likely was involved. They've been around since 1934 helping customers figure out what parts are universal to multiple cars and trucks. Hollander is a staple of the auto recycling industry.