new alternator/muffler = higher rpm?

so i got my boat back from being fixed today (2005 nautique sv211) and it got a new muffler and a new alternator. when i put it in the water it was running at a much higher rpm than it used to..1100 as opposed to 800 when in neutral. also, when i was flushing the engine after using it (saltwater usage) it was running at 2000 rpm just sitting at the dock when it used to be just 800. the throttle in general was much more touchy. im wondering if the new parts could be reason for this and if it is bad? it seemed like the boat was running fine, just at a higher rpm. anyone know anything about this? thanks guys.

This is why I hate fuel injection. Crazzy little problems like this for no apparent reason. 1100 RPM and I might say check coolant sensor(s) to be sure the engine knows it's getting warm. That amount could just be a normal high idle on a cold start and it never figures out the engine got warm. 2000 RPM, not so much.

I'd check for obvious stuff, like that your throttle linkage is working and not loose. Remove the air filter and be sure the throttle body is closing fully when you bring the throttle lever to neutral, and that no junk got in the throttle body keeping it frmo closing. Also be sure your return spring (if you have one) is still attached. Check for vacuum leaks if you have any rubber vacuum lines on the motor. All that aside, I'd look at the IAC. Could be plugged and sticking open or the wiring could be bad leaving it open. Try unplugging the IAC and starting it, idle should be lower than plugged in.

Just a few generic thing off the top of my head, hope you find it. If it's nothing simple like what I mentioned I'd bring it back to where you got it serviced and tell them what's happening.