1994 Honda Civic overheating

I just bought a 1994 civic ex (140000 miles on odometer but the motor has been replaced). The origional owner blew the last motor by running it w/out oil and water so they replaced it. The replacement engine sounds great, but when I drive it for about 15 minutes on the freeway and sometimes on the street, it overheats. Also the heater does not blow hot air. We've replaced the thermostat. The fan comes on for about 20 seconds at a time, but I think it comes on later than it should and not for long enough. The radiator stays full and there appears to be no leaks. We bled the bleeder valve for air in the system. After it starts to heat up, I get power loss and it starts to sputter while driving and feels like its gonna cut off while idling at stop lights. We are going to use some radiator cleaner and run a toggle switch from the fan so I have full control on it. We'll see if it helps, but if that doesn't work I have no clue what to do or what it could be. Please help.
Aaron