Lots of in-and-out is necessary for custom systems in tight confines. Wallach makes the cope in the passenger-side downpipe where it mates to the crossover pipe with a grinder.
Tailpipes: Resist the temptation to call it quits at the muffler (unless using glasspacks with integrated turnouts). Tailpipes should always be included: They channel deadly carbon monoxide away from the cab.
Headers/Exhaust Manifolds: Primary-tube clearance and collector dumping location are the main concerns. The three most common solutions to literally starting a custom exhaust are (1) finding an OE answer, (2) sourcing aftermarket "swap" headers, or (3) creating custom headers. In the OE realm, Chevy small-blocks are the ideal example of multiple manifold configurations for the same block: Car, truck, and Corvette manifolds vary in their dump locations. Research and possibly junkyard foraging are required. Less mind-numbing are swap headers. The aftermarket offers these for popular repowering combinations.
Odd-ball swaps can require starting from scratch. For example, someone who's dead-set on putting a Caddy big-block in a flatfender will likely face a few exhaust challenges. Luckily, header flanges are available for many engines. Existing headers can sometimes be modified and welded to these flanges. Alternately, build-your-own kits are available; a few companies even make custom headers.
Emissions: For vehicles that must pass "smog" testing, catalytic converters can add considerably to exhaust-system cost. Even ones that don't have to pass but have closed-loop computer-controlled engines need exhaust bungs for their O2 sensors.
This rearview shows some of the cuts and bends necessary to fit 2.5-inch-diameter tubing in tight spaces on a YJ. A transmission swap with an externally mounted clutch slave cylinder (upper right) imposes a heat-sensitive obstacle. | 
American Offroad located the catalytic converter above the bellypan. This protects one of the system's most expensive components. | 
Here, the best location for a quiet (big) muffler turned out to be on the driver side in front of the axle. That way it clears the rear driveshaft and X2 suspension kit's passenger-side-mounted Torque Fork traction bar. |
Pro Tips
American Offroad offers these hints, derived from 16 years of trying different approaches.
Tools: No bender or notcher is required. Wallach claims that tubing can be coped with a grinder in less time than it takes to set up a notcher. For cutting, he prefers a portaband or even a reciprocating saw over a chop saw.
Hardware: Use the thickest available flanges and hangers. Avoid parts-store exhaust hangers-source minimum 3/16-inch-thick hangers for durability. You'll also use fewer since heavier-duty hangers can support more weight.
Sealing: Prep flanges' mating surfaces on a belt sander with 80- or 100-grit paper. Use name-brand flange gaskets reinforced with Ultra Copper silicone gasket-maker. American Offroad double-nuts flange bolts as a third line of leak-defense.
System Design: Wallach prefers the cut-and-tack approach: "Eyeball the angles and keep cutting until it's right." For optimal flow, he recommends butt welds, which require all gaps to be less than 1/16 inch. Otherwise, the joints are susceptible to leaks, and the welds create heat-stress points at the tubing's edges. If using slip-fit swedged joints, always go male-into-female following the exhaust path. Otherwise, leading edges slow down exhaust flow.
To clear the long-travel suspension components, American Offroad routed the tailpipe back out the passenger side. A stainless tip gives a finished look and fights rot at the end of the system. | 
High-temp paint adds a layer of corrosion-resistance. It also gives aluminized tubing a finished look. | 
The finished system features grounded-smooth welds, painted tubes, and double-nutted flanges. RTV silicone on flange gaskets ensures a leak-free seal. |
Contrary to traditional thinking, true "dual exhaust" systems-where both sides are independent of each other-usually don't work as well as systems that have a balance tube/"H" pipe/crossover pipe. Since compression and exhaust scavenging vary among cylinders, tying the sides together equalizes the pressure. Performancewise, this smooths flat spots in the powerband and also controls back-rap that can result from abrupt deceleration.
Finishing Details: Stainless steel is virtually maintenance-free. People who want to send out their systems for thermal coatings should add flanged joints at accessible locations. For custom headers that will be thermal-coated, Wallach recommends TIG-welding all joints for aesthetics. Otherwise, a coat of high-temp spray paint makes aluminized tubing look finished and helps retard rust.
The photos here show highlights of American Offroad's custom 2.5-inch exhaust for a YJ that has a swapped-in Vortec V-8, an AX-15 transmission with remote-mounted slave cylinder, and a Black Diamond X2 long-arm suspension system. Short-wheelbase Jeeps' tighter confines present more logistical puzzles, but the overall approach and execution apply to all 4x4 custom-exhaust jobs.