I've contemplated this question quite a bit. I'm in Ohio and also looking at buying 50+ year old forest (not really virgin, but about as close as we get in most of Ohio). I think that in terms of long term, it would be easier to start from forest than from bare ground. There will be a better ecosystem and an upper canopy layer (as well as many native fruit/nut shrubs/trees/herbs). I am interested in getting around 100 acres and eventually managing the entire system as a food forest.
I do think that it would involve quite a bit of tree thinning/removal. You need to provide a fair amount of light and edge to grow many plants. Ideally (as another poster mentioned) you could use goats or other forage animals to control resprouts (and perhaps use some coppicing as well). I've had a fair amount of success on the small scale mostly clearing an area (leaving a few value trees - which could be virtually anything depending on what you want out of it, legumes, nut trees or timber trees) and then planting below them. I also planted some trees that I plan to eventually become upper canopy trees (at which point I will probably remove some of the current upper canopy trees). All of the cleared wood can have a purpose though (left to rot and decompose, made into hugelkultur on the spot or moved, or used for building or sold for timber). Also if you pull down the tree (rather than cut it), than the root ball that comes up could provide an instant hugelkultur - or at least a very nice start) and the depression left behind would provide a small water collecting hole (more edge). I plan to use machinery (and already have on smaller scale), but I think you could manage 20+ acres without machinery (other than perhaps a chainsaw), provided you only worked on a few acres at a time (begin a food forest from one acre, than move on to the next acre while maintaining the first one etc...).
Downed wood I think could be left (it should as it decomposes provide similar benefits to hugelkultur), but piling soil on it would probably speed the process. High value wood would probably be sold and removed.
If you are buying a large amount of land than things like walnuts (and other normal
permaculture "problem" plants) are much less of a problem. If an area is concentrated with walnuts leave them be and let your animals forage under them. If there is a stray tree far from the large population you could probably also just let it be (yes it will effect other nearby plants, but the area it can effect will be relatively small). On my 5 acres right now I leave things like pines trees, but cut down a few per year to provide winter goat forage (than plant blueberries in the openings).
Since you mentioned deer/coyote, I've been contemplating this and perhaps I can get some feedback on the possibility of it working. Around the border of the land, cut out say a approximately 100 foot swath. The regrowth would provide a fairly dense thicket. If you were able to add some thorny plants (osage orange or locust) into that thicket. I imagine it would provide a reasonable barrier to wildlife. It probably wouldn't stop them (though I imagine with a bit of work it would be able to use that thicket as a
fence for some animals), but it would slow them. Especially if there are some wild fruit/nut trees/shrubs mixed in (with luck they would already be there with no help from you).
In terms of permaclture ethics. First I'm on the Paul Wheaton side of I don't care that much, if I can make a bunch of money and be a lazy farmer (do nothing but harvest - eventually) than I will be happy. But 2nd in many heavily forested areas a meadow with a lot of fruits and nuts would provide excellent animal habitat, better than the forest itself in many cases. Though they may not be the final stage of succession, meadows and prairies are natural even in forests and they provide habitat to animals and plants not suited for forest. I think that the argument could be made that a 50+ year old forest will provide the most benefit if left untouched, but I also think you shouldn't feel bad about touching it if you are providing good wildlife habitat.