Here's what I learned from recreating someone's Minecraft version of Mann Manor:
48 units per block side is the golden rule. Just big enough to bump your head on a two-block doorway, just small enough to see over a block and a half, just like in Minecraft, and with 3 units per pixel you can build everything from fences to tracks without going off-grid.
Block sides should all be aligned to Face; undersides should be aligned to World.
Even if you had an automatic converter that tries to consolidate blocks into large brushes, it's not likely to break them up in the most ideal way, especially for splitting the brushwork between func_detail and world brushes. Best to do everything manually, but mocking up the whole thing in creative mode first is still a good idea. Should help keep you in the "building things in Minecraft" mindframe while you're designing, if nothing else.
Trees have to be models because face culling would toss out all the internal leaf faces otherwise, even with every block func_detailed separately. Likewise torches should probably be models with no collision meshes. Fences work best as models for lighting purposes.
HDR should of course be avoided, since it's not in Minecraft itself, but -staticproplighting is a must for those trees and fences.
Clip your stairs as you would normally, but for stepping up onto single slabs, as well as the bottom step of a staircase, you may prefer to place a clip brush stretched across the front, 12 units high and one unit thick, to emulate players' ability to automatically step up onto things like sidewalks despite being over the height limit for that. Player models floating above the gap between steps is a lot more conspicuous when they're 24 units apart.
One of these days I plan to compile all my textures and models into a resource pack and release it. It's not finished, at the moment; I need to hunt down a good pixel artist to make some custom item pickups, and get a complete set of particle effects.