My BF9.9 stopped spitting so I took the thermostat out and there was salt and other stuff around the thermostat. What is the next step to cleaning the cooling system?

Pull the thermostat out and clean it up well. Push on the back against the spring and make sure it opens smoothly. If there's crud in it that would prevent it from opening or closing all the way, it isn't clean enough. If in doubt, replace it.
If you're not sure when the last time the impeller (water pump) was replaced, it's a good idea to go ahead and replace it. This is a bigger task if you haven't done one before.
Also, sometimes they really are pumping but the pee tube just gets clogged with salt or corrosion. To make sure this isn't the case, either run a small wire up through the pee tube to clear it, or force compressed air back through it.
Good luck.