SW Black Fox or SW Iron Ore for all the Rust Brown you have .

if any of the wood is natural, I would Leave it, like over the windows and that beam at the entrance... Paint the entry door a light color like the cactus Silvery Blue/Green

Natural Wood Beams are a beautiful accent, but since yours are already painted... you could mimick a stain color with a solid stain, or paint color in a wood tone like above...

The wood has been stained a couple times and is a orangey brown stain that is peeling/fading. It needs to be restained. What color do you recommend?

Is a metal roof out of the question, budget-wise?

It appears from your landscaping you live in very hot climate so I think you should prioritize a cool roof, when usually means picking a very light color. Then if you think you need facade color changes to be more harmonious with the roof, do it that way.

MCM or midcenturly vibe seems to be a popular idea but is unclear whenever anyone uses the term, especially since your unique house has features that simply can't bring the house into "reading" MCM. It appears your house has additions that also take it rather far away from craftsman, so just go with what works for climate, budget and whaever looks best on your unique house given those limitations.

That is a great looking house, and I like mytwo cents' suggestion of a metal roof

IMO embrace what you have and for sure it is not MCM and not sure what MCM tradional would be . The house looks to have a bit of a personality issue for sure . I would at least do all the siding one color and probably all the wood trim the same color. That would simplify the exterior so at least a bit better look.I agree to a metal troof if the budget allows . I just used Racoon Fur BM on my siding on my very MCM ranch we have the old 50s stucco with bits of black glass in it and the RF looks awesome with it. The rest of the stucco prety close to the color of your stone .