3d Printing...To get a printer big enough to do a set of flares on the TJ, it would be not something that you are going to buy for yourself. So, you're looking at a two or more piece design, that would need to be joined together. there are numerous ways to do it, but I don't think any of them will look good. 3D printing is also VERY slow...you'll probably have 24+ hours into printing one flare.
Urethane is probably the way to go, but you'll have to contact a model shop to make a mold, and they will need a PERFECT set to make master. The nice thing about urethane is that its a Thermoset plastic instead of a thermoform. Urethane specifically can start as a liquid, so once you have the mold, you just pour it in and let it harden. You might be able to cost effectively do that. I'm guessing here, but I bet the reverse engineering and mold build would be around 25K to have done. Remember, you need FOUR molds...not just one. Each part is specific, front to rear, right to left. If you got 25 "shots," you'd have to charge 1000 bucks each just to cover your engineering costs, then tack material on top of that.
You start talking about ABS, nylon, or other type Thermoplastic and you're talking injection molding. GREAT for large part runs (10,000 is a low production quantity). It can produce a part very inexpensively. However, the molds are VERY expensive. So, your up front tooling is going to be ridiculous. Probably $150,000 or more (they are not real simple parts to make).
If you really want to chase this down, Composites are probably a viable option. Fiberglass is simple, but heavy. Carbon fiber would lay up the same way, would be lighter, but its also stiff.
If you want to experiment a little bit, grab a heat gun and a sheet of acrylic (plexiglas) from the hardware store. Give yourself a straight line, heat the material along the line, gently, with the heat gun. After a little bit, fold the plastic. You can make a pretty nice plexi box that way.