Why is my turntable sounding so muddy?

Did you remove the belt when it was put in storage? It's common to have a problem with the belt when a turntable has been in storage with belt installed.

if you plug to the wrong input MM instead of MC or visa versa, than your TT will sound muddy.

another cause can be a buildup of gunk on the stylus. The big wads are easily seen but i have noticed a buildup can cause the sound to be muffled or muddled. A little Magic Eraser can remove that from being a source of the issue

Thanks for all the positive feedback. I tried a few things that you guys mentioned and the one thing I did was put the original cartridge back on.
It sounds better but still not quite what I think is correct? My next move is new tubes I will give that a try. Czarivey your thought is the one 
I thought about and that is why I went back to the original cartridge. I don't have the manual on my Counterpoint SA3 and looked on line for where the setting are but no luck yet. Again thanks for you help.

Could there be corrosion on any of the connections?  Maybe it's time to clean the contacts?