Disorganized brain dump, part 1:
Of the two parts you want to make, the flares are probably the easier part to make if you're wanting to use fiberglass for the mold and the parts.
If you have a set of flares that you want to directly copy and that are already mounted (so they are the proper shape), make sure they're properly surfaced with body filler, high build primer, etc., and painted so you're starting with the best possible finish. You can correct stuff in the mold later, but the better your starting point the better the mold will turn out in the first place.
You'll also want to give the fender flares a bunch of coats of good mold release wax, like 5 to 10 probably depending on the wax. You're sealing up the surface pores and building a good wax film thickness.
Epoxy usually works the best over painted stuff, because it doesn't have solvents like the styrene monomer in polyester resin that can soften fresh paint. But, epoxy is also usually a bitch to polish out, and it's also relatively expensive. There are brush-on gelcoats in both epoxy and polyester available, both of which will give a good hard surface that can handle sanding and polishing. That's obviously the first step. There are polyester gelcoats that can be backed with epoxy, and epoxy gelcoats that can be backed with polyester, to take advantage of certain strengths/weaknesses that I won't go into. I'm just illustrating that things need to be chosen to work together, so don't just grab a bunch of stuff without verifying.
If you're using polyester resin like a nice isopthalic tooling resin (low shrinkage, strong too), you'll need to back the gelcoat with a surfacing veil or some lightweight fiberglass chopped strand mat (CSM). This adds some stiffness behind the gelcoat to help prevent print-through of the rest of the layers of fiberglass when the resin shrinks a little. Then you add a few layers of regular fiberglass mat, and then can back that with heavy woven fabrics or stitchmat to bulk out the thickness and make it stiff.
It's sometimes a good idea to add some stiffening ribs out of plywood or MDF, which can be laid up onto the back of the mold with more fiberglass mat and resin. The ribs can also act like table legs when you make parts in the mold, and keep a long skinny mold from twisting without having to make the mold into a battle tank.
Adding a flange around the edge of the part while making the mold is a good idea also, whether that's adding a piece of aluminum sheet in the wheel well area and then using the metal fender to make the rest. This gives a support for the fiberglass when you're laying up the parts, as unsupported cloth/mat hanging over the edge can pull away from the mold surface under its own weight because it doesn't like to bend around a corner. That's a pain in the ass. You can blend the flange material to the flare with a little bit of modeling clay or some pattern maker's fillet wax (kind of like caulking the trim molding before painting a wall in your house) before making the mold off of the flare, then the flange gets laid up in the mold.
You can't use fiberglass mat with epoxy, because the binder that holds the fibers together won't dissolve in epoxy. No biggie though, because epoxy has extremely low shrinkage and lightweight cloth is usually fine without worrying about print-through of the cloth pattern.
The molds finish the same way as automotive paint, with sanding/cutting/buffing/waxing. You just need to find products that are compatible with the gelcoat you're using, and again beware of epoxy gelcoats unless you know they can easily be sanding and polished.
For the actual parts, cheap stuff with complex shapes can be made from cheap polyester resin and chopped strand mat. Not very strong. A good polyester or vinylester resin along with fine weave fiberglass cloth (like 8HS, 8 harness satin) can make very strong parts that are also flexible and can take some impact if they are thin. Cloth can sometimes make it difficult to layup things like recessed bolt bosses, as the cloth doesn't stretch and can't shift around like CSM, so part geometry (or proper workarounds like smaller pieces of cloth) need to be thought out. You can gelcoat the parts if you want too, either by spray or by brush. That goes against the mold surface first, then the actual resin and reinforcement.
Epoxy also works, but again make sure you know what you're buying and if it is well suited for what you're doing.
The gauge pods can be made of fiberglass too, but you need to choose thin fabrics, etc., that will conform to the smaller/tighter/sharper contours of the pod.
If you have a CAD file, you can also have a wooden mold for thermoforming made on a CNC router, or out of epoxy block on a milling machine. A lot of cheap add-on flares (think textured ABS) are made with thermoforming, and it's pretty easy to add features like those ugly screw countersinks for easy mounting. Just a mold on a flat base, with some small holes drilled all over the place for vacuum bleed.
A ton of gauge pods are made with thermoforming as well. Super cheap to make. The better ($$$) pods are often injection molded, because then you can add ribs, panel clip bosses, screw bosses, etc., to the back side that you can't easily do with thermoforming or with a fiberglass part.
I have done something like this with resin casting, but making multi-piece molds for thinwall resin casting is not something for a beginning project.
There are definitely places that can 3D print the pillar pod in a single piece, and I wouldn't be scared of making smaller pieces and post-joining like mentioned already in this thread.. You'll likely be vinyl/cloth wrapping or spraying it with paint or vinyl dye, so it should be somewhat easy to hide bonded joints. Same thing with getting rid of layer-steps; you can sand them out or coat with high build primer and sand to finish if they aren't going to be vinyl/cloth wrapped.
Also, you can do all of those cool ribs, etc., on the back of the part like you could with injection molding.
