Discussing “Plan A” with my mechanic of many years regarding a hole in the flex joint of my Trooper’s exhaust system, I asked, “What if I got a custom job, headers to tail pipe?” He said, “No way. Emissions specs are set by the mfr and sent to EPA… you won’t pass Va. inspection.” I’m thinking, how’s that, when see all sorts of non-OEM exhausts, rims and tires on all sorts of vehicles?
You can usually change what you want aft of the catalytic converter as long as no emissions equipment is involved. If your Trooper has an emissions inspection, they often look for unauthorized alterations to the rest of the system. Rims and tires aren’t covered.
The leaking flex joint could be removed and replaced with a rigid pipe section. That will not cause you to fail an emissions (or safety) inspection. However, the flex-pipe was there for a reason (vibration isolation) and by removing it you may create objectionable noise and vibration problems. You neglected to mention model year and mileage, but if the entire exhaust system is questionable and repair impossible, a new custom system (forget the header) from the manifold back, if done correctly, is legal and will pass emissions tests…Any good exhaust shop knows the drill.