Lou - I'm not sure about all the specifics, but I'll answer your questions as best I can.
I do not know about the dredging laws, but I would tend to think that they would be frowned upon by the Army Corps of Engineers (ACOE) If the stream is not a juristicional stream (shown as a blue line on a USGS Quad map) then your chances of being able to modify it are greatly increased. You'll have to do some research into your local wetland and stormwater rules to find out exactly what you can and cannot do.
The devices you mention to armor the banks are effective, but not the best option. If space permits, your much better off building a smaller channel with a floodplain and letting the stream use the floodplain during storms. This is by far and away the best way to protect against the erosion. By giving the stream a well vegetated floodplain to use, you slow down the velocity of the water.
In our restoration work we will generally protect the banks on the outside of bends with rootwads (take a 18" diameter tree that's been pushed over - not cut down - cut it off so it's only about 20' long, and jam the trunk into the banks,leaving the roots exposed on the outside of the bend) not only does this help keep the bank stable, but it also will provide better fish habitat. We'll also use rock vanes which are a v shaped rock formation in the channel to funnel the water to the center of the channel. This essentially steer the water around the bend, instead of letting it slam into the bank.
I have seen most projects funded by state funds, but there are some federal grants out there - one example is the recently passed Farm Bill - but I don't know if they are available for golf courses. If you go to the respective agencies, and sho them that you'll be establishing a natural buffer and wetland area, they might be more willing to help out. Especially since you've lost some wetlands with the dams failing.
If you want some more info I'd be happy to help where I can, If people are interested let me know and I will try to post some pictures of these examples in the near future.
Derek - just a couple thing I want to note about your post. Armoring the baks with rip-rap or RR ties does not slow the water down at all. It just give the banks a higher permissable shear stress. It's effective at protecting the bank from erosion, but generally just causes more problems downstream of the project.