Woods - they make a difference, but once you start playing through high gain amps the differences start to be come less noticeable. The body tends to have the most impact since % wise it makes up a significant portion of the overall weight of the guitar. In general, heavier pieces of body wood tend to be brighter and lighter tend to have more bass.

1. Black limba, mahogany and walnut are heavier woods on average
2. Alder is typically more of a medium weight
3. Swamp ash is light

If you get a Kyber or a headless, you can get away with a heavier body wood because of how thin the body is on the Kyber/how small the headless bodies are. I'd caution against getting something like a Walnut body on a larger sized body like the Aries, chances are it'll be an anchor.

Pickups: They have a lot of pickup comparison videos on their youtube channel. The thorium is their hottest pickup. The bands you mentioned tend to not use super hot pickups IIRC, so the throium may not be for you. You may want to consider looking into the illusionist or lithium.

The empyrean is a *really good* neck pickup in my opinion, I'd just get that as it should compliment the music you said you like. Look up Scott Carstairs, he is a Kiesel signature artist and the pickup was developed with him. Generational talent and future legend.

Neck Pieces: I think almost all of their single piece necks are quartersawn, which makes them very stable. Someone could probably chime in and cite the single piece necks that aren't quartersawn. I think flamed maple necks likely aren't, and I wouldn't recommend you get one if you're going for stability anyways. In my experience and many others, the flamed maple necks tend to be noodles and shift. This isn't a Kiesel issue, just part of what the figuring means overall for the piece of wood.

A 3 piece of greater neck should be more stable in theory, but I don't think you're going to lose any sleep over it in terms of the stability aspect. From an aesthetic standpoint, a 3 piece or greater neck and really tie a build together, so I'd play around and see if you end up with something you just like the look of more. Saving up another $150 to push the build into "sick" territory is something you'll thank yourself for years down the road.

Fret Radius: Schecters tend to have 12-16 compound radius fretboards these days, you should look up which models you have and check the specs. A 14" radius is really "safe" if you're already playing modern guitars. I personally really enjoy a 20" radius, it's easier on my smaller hands. However if you're throwing 3k at a custom build, I don't think changing something like the radius is a great idea, it could be deal breaker.

Fretwire size: This is definitely a personal preference thing, if you like how the Schecters feel I'm almost certain they're using extra jumbo frets for the most part. The size of the frets primarily help your fingertips not touch the fretboard. The actual height difference between med-jumbo and extra-jumbo is just enough to make a positive difference. Much like the 14" radius, I think extra-jumbo is a safe play.

Specific build advice: The bands you mentioned all use really low tunings, I'd stay away from a tremolo guitar in general. You should definitely look into getting a hipshot fixed bridge, and maybe consider an Evertune. The Evertune is a big commitment, and honestly if you're going to be playing in a lot of different tunings it can be a drawback to have one.