I was at KSC for 4 days last week for the SpaceX Pad Abort Launch. I had lots of free time and spent 3 days at KSC, a day at the Cape Canaveral Air Force Museum (which you can also see as part of the KSC Cape Canaveral Then and Now tour), and the Astronaut Hall of Fame in Titusville (3 hours is plenty).
If you only have one day, do KSC with the Saturn V tour (included in admission). I did the Launch Control Center tour which was neat, but if you can only do one other tour definitely do the Cape Canaveral tour. I had done that tour before but this time I had a press pass so I was able to go back out on my own and spend all the time I wanted. I spent about 4 hours in the launch control centers, museum, and mostly in the rocket garden (where everything is just rotting to pieces) and at the Redstone pads.
At KSC, they have Atlantis (the intro to walking into the display was stupendous, the best display ever of any space artifact, ever), the Apollo 14 CM (average display), and Gemini 9 (horrific display, not even a sign saying it was Gemini 9). At the Astronaut Hall of Fame they have Schirra's Sigma 7 (worst lighting ever, just bizarre) and Gus Grissom's Mercury Suit (helmet is not the original and the suit is starting to discolor, also incredibly poorly lit). Sigma 7 is very cool, though because a number of exterior panels have been removed (for reasons unclear) which allows you to see some of the thruster innards. But so poorly lit I had to use my cellphone light to really see things.
Overall, the KSC museums are truly incredible.