Michael's suggestion is a good one. You can't go wrong with the big black book.
You are asking some very specific questions about a very broad subject, but I will try to list a few, if I am understanding you correctly.
You could take the example of a homestead and break it down in parts, perhaps a homestead with a number of livestock, alley cropped pasture, and a pond system, say.
So strips of perennialfruittrees and bushes on contour add texture to the land, breaking up sustained winds and sheltering sensitive crops, reducing wind dessication, catching airborne particulates and adding them to the soil. They also feed the people that tweak the permacultural system to provide more than it would on its own, and, due to the heavy fruit focus, be a source of food for many pollinators, so keeping bees would be another possible element with a number of functions, including honey and wax production and pollination services.
Alleys of pasture between these and, say, rows of raised garden beds (think large ones, hugelkultur, on contour, initially made with large equipment) add pastoral diversity of grazing for, say, a small dairy herd (a small traditional breed, and no more than two cow/calf pairs), a small herd of dual-purpose sheep, a rabbit tractor, and a chicken tractor.
Grazing each of these in succession (with the chickens last, and following within the hatching cycle of cow and sheep parasites) would make full use of a paddock-shift system, remove larval parasites from the dung left on the pasture, break up and distribute said dung to help fertilise the pasture, and feed four different sets of livestock with little to no supplemental feeding required (I would always keep some amount of feed available, simply as an indicator of livestock interest; if the piece of pasture they're on is less interesting to them than the feed bag, it's time to move to the next paddock).
Aside from dairy, fibre, and meat, these livestock also cycle the nutrients of the paddock system much faster than if they had all been left fallow for a season, creating fertility faster than otherwise possible. People are indeed using mob-grazing and paddock shift systems to build soil. One such, if you aren't familiar with his work, is Joel Salatin.
Paddock shift grazing patterns stack functions simply by providing 30 days of disturbance-free regeneration (let's say that's how long each paddock regenerates in this system before seeing livestock again) for ground-dwelling animals and insects to use, and I would be surprised if those populations didn't, over time, clue in to the nature and sequence of the system, and adapt to it. Allowing a full regeneration also stores more carbonunderground, due to increased root zone health and growth.
Keeping a pond system in the permacultural fashion can add protein through fish, aquatic plants for human and livestock consumption and/or mulch, holding water in times of drought, fertility through use of pond water for irrigation (depending on how stable or sensitive the pond system is, this may not be possible) or simply increased soil life around the perimeter of said ponds due to more regular moisture levels.
A shelter belt on the windward side of the property, let's say one based around a Jack Pine Boreal/Temperate Hardwood Transitional Forest guild, could not only be the first defense against the effects of severe wind, but could easily be your planned zone 4-5, where you do much of your planned wildcrafting, including potentially the harvesting of culinary fungi, like Chanterelle mushrooms (my favourite, and where I'm from, symbiotically linked to Jack Pine, and also worth a lot of money in stores), or any number of others.
I am probably missing some of the function stacking that's going on in the system I just described, because good systems complicate themselves.
The next area into which function stacking moves is the adding of value to raw materials coming from the system. This includes preservation of food goods through canning, drying, curing, or for meats charcuterie, smoking, curing, other forms I am probably forgetting, the cleaning, sorting, processing, spinning, and weaving or knitting of fibre goods, the making of cheese, brewing of beer, wine, and/or ciders, etc...
I am leaving out selling raw goods for profit, like eggs and honey, which is another way of filling functions, and sometimes the best way. I mean, if you were really good at producing honey and eggs, and you could feed your family better focusing on honey and eggs, your returns there could easily be reinvested in the homestead.
These are also all examples as to how it might be difficult to pidgeonhole elements of systems as either elements or functions, as it's rarely so clear-cut as, say, keeping the top of your rocket mass heater riser free to boil your kettle as you warm your bum on the warmed mass.
I do hope this is some use to you, though, and if you ask more specific questions, I am sure many people on this site have good examples for you.
A human being should be able to change a diaper, plan an invasion, butcher a hog, conn a ship, design a building, write a sonnet, balance accounts, build a wall, set a bone, comfort the dying, take orders, give orders, cooperate, act alone, solve equations, analyze a new problem, pitch manure, program a computer, cook a tasty meal, fight efficiently, die gallantly. Specialization is for insects.
-Robert A. Heinlein
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