Where is safe to step on in attic

Other than the part where you are putting Romex (NM-B) in the conduit, I not only like your plan, I'm doing something like it myself.

I've seen too many rodent-chewed wires to be overly comfortable any other way, no matter if code would find less protection acceptable. I don't find it acceptable, and the cost is not all that great.

If the conduit is sized for the NM-B (as a round wire the diameter of the large dimension of the oval) you CAN do that, but it's miserable to pull and inefficient (of conduit size) .vs. just using THHN when in conduit. If leaving conduit, make a junction in a junction box when transitioning to NM-B.

While not having rodents in the house is a great idea as well, it's one that's hard to guarantee in practice over the long term...

Cleaning up

Pro: Reduce fire risk from scrap kindling material.

Pro: reduce wildlife habitat internal to house.

Con: It's work. Not that much of a con.

Painting

Pro: easier to see (if you paint it white.)

Con - expense (money and time) .vs. amount of time you'll spend in it, since it does not appear to resemble living space or enough space to convert to living space, unless you are housing hobbits or leprechauns.

There is no real benefit to "sealing the wood" since there should never be weather in here. Kept dry, "unsealed" wood lasts for hundreds of years.