When I say get the shocks "done" I'm talking about having a pro valve them for your weight/riding style. From the factory the fx nytro has a very flat rate valve stack. It seems very stiff, and keeps the sled sitting high in its travel. It rides really rough in the small stutter bumps, and takes the larger bumps fairly well, but does blow through its travel easier than I thought it should...considering how stiff it rode in the small bumps.
Have the guy who valves your shock put some progressive valving in them. make it ride a little softer in the small bumps, and progressively get stiffer for the large hits. You shouldn't have to explain this to a guy who is a real professional, he'll know exactly what to do. Tell him your weight, and that you are an aggressive trail riding, maybe you do a little jumping and stuff. Whatever you want to tell him.
It made a huge difference when I did this to my nytro. It rode nice and smooth through the small bumps, but still took the big hits like a champ. But the biggest improvement I thought was in the cornering...it actually cornered now.
I tinkered with the nytro for two full years before I gave up. I had it working pretty well, but it was still a bear to run through the woods hard trying to keep up with the lighter sleds. The beginning of the 3rd year I had the rear shocks "done" and never touched anything. Installed the shocks and my brother ran it all year. It was a whole new sled...that actually worked.
I wouldn't own a set of Fox Float shocks unless they were at least the X models, or the Evols. The X shocks are really nice, and work great. I imagine the Evols work even better. So I do suggest getting Fox Float X or Evols, however you decide to do it.
My brother had a 2006 nytro RTX, it had the same junk shock valving as the fx nytro rtx has. Yamaha doesn't know how to valve shocks. Even the old SX-R sleds rode like crap, but once the shocks were valved they rode decent. But there is a reason my SX-R 700 has a extra-10 suspension in it.
I don't do my own shock work, I'm no professional, but I have spent a lot of money on shocks.