Hmm, my comments may be misguided due to my plains dwelling experience, but the primary thing with navigation is that the trees appear to be changing paths to hinder orcs and help elves so following and navigating by paths is a bad idea. Whereas ignoring the path and going by bushwhacking orienteering seems like it avoids a lot of the problem.
Orcs, in this setting at least, are a very succesful underground/burrowing race. And tunneling doesn't take that long compared to the length of the engagement.
Elves can put nasty creatures in your holes but you're in their first and that's a tremendous advantage. Tunnelling is just a good idea if you've got the numbers, the will, and the expertise. The history channel has convinced of that much at least.
Fortifying the river strikes me as very expensive. That ties up a lot of men, stretches them out, and makes them vulnerable. Plus you have to put up a lot of infrastructure in enemy terrain. And if they capture your fortifications you are in a whole mess of trouble. Burrows are easy to make and abandon or destroy, and they are there primarily to protect and hide your men, a fortress is a whole other problem.
Plus it's a river, do you really need to do more than be able to get people up and down it? If you've got the chokepoint fortress neutralized and control the other end then it seems as though every other effort you make is going to cost you and only hurt the elves a little. It's not like you can seriously challenge them for control of the forest, and it's not like they can do anything at this point other than run supplies and men across it.
Double plus, deforesting the river banks is gonna give you nightmares as the rivers course, clarity, and navigability change with the ecological change. You're talking insane bank erosion, unpredictable flooding, and having to put together a massive engineering project to control and/or avoid that.
Smoke from burining, on the other hand, can be nice.
If the river is pretty navigable aside from chains and vines then I think you simply need to convoy large amounts of ships. Since the orcs control the rest of the continent and river boats aren't exactly supremely expensive I think you should just accept that you are going to loose a lot and that you can make taking out a convoy a very very expensive enterprise for the elves.
In terms of supply, you do have the problem of having to bring most of it in and they're being a lot of you. But you are melee infantry with equipment adjusted for endurance not excellence which could also be said of your troops and not at all said of the elves. On a one for one basis you need it less urgently and can be more effective when in poor supply. So more or less a moot point other than to say that you should probably adopt a strategy of bringing more than you need, planning for less than you would want, and making the supplies as horribley unsuited to the Elves as possible.
Chain breakers on the ships is an awesome idea.
And it's not that you would lie to the trees, though that is theoretically possible, it's that you provide with as much confusing information as possible. They are trees, they can't be that discerning no matter how perceptive they are. March in big dispersed groups and make certain that everyone is very aware of how they move above ground. Have long periods of quiet and pattern and when you do move move everyone at once with lots of feints and chaos. Move all of your posts around frequently and try to make your patrols random and very broad and dispersed. And don't be stealthy be loud and confusing. If you convince an elf sniper or ambush to move you've already done a lot of good.
And they will move, it's not as though they can afford suicide missions.