My 95 Baja w/350 mag mpi's ran very rich after driving it for about an hour barely idles and black smoke out exhaust, but clears up after 2500-3000 rpms someone told me dirt in injectors.

"barely idles but clears up after 2500-3000," is a classic water in motor symptom. You should also check for signs of water on your spark plugs. Possibly leaky riser or gasket.
Jim

Check your cooling system for restrictions at idle and replace the CTS before tearing into the exhaust system, check spark plugs anyway.

Purely a guess, but my first thought is MAP sensor.

Rene

Check plugs all carboned up and somewhat wet (gas) Marina says he hooked it up to the scan tool no codes and all sensors working normal hopefully he's not lying, but I trust him.
I also heard might be VST getting clogged.... dont really know

Not a clogged VST. Clogged VST will idle but fall on its face when throttle is applied. My expierence anyway.

Thanks for the help everyone Just wanna still use the boat while there is time left. I'm just going to leave it at the marina til the find the exact problem

Running to rich, replace CTS.

It's running very rich black smoke barely idles . Would a CTS make it run that rich

When they had the scan tool on it, what was the injector pulse width at idle? Thats the first thing you need to look at to see if the engine is being "driven" rich by a bad sensor or if it's a mechanical problem such as high fuel pressure, leaking injector, failed mech fuel pump, or overflowing VST.

Dave