Rep Power: 0

So my civic has been sitting for like 7 years and I finally got the car to start after fixing some chewed up wires, and changing fluids. The only problem is after 5 minutes of just idling the engine starts to overheat. So the fan doesnt even turn on so I replaced the thermostat and cooling fan switch, and the fan still didn't turn on. So I put a paperclip in the wire connector that turns the fan on and it spins. Even when it spins, the engine is overheating. The coolant is full, I have filled it up and got rid of the bubbles after replacing the thermostat. Could anyone help me figure out what to do??

 
Rep Power: 126

Is the overflow reservoir filling up?

 
Rep Power: 223

This, this is critical information

 
Rep Power: 211

Did you replace the thermostat? If it overheats fairly quick from a cold start it's most likely a stuck closed thermostat.

Did you do a proper coolant system (air purge) bleed by raising the front end on jacket stands to a point in which:
1) the radiator neck is higher than the valve cover
2) climate control is on max heat and fan off
3) from cold start with the radiator cap removed let engine idle until radiator fan engages (roughly 20 minutes), while adding coolant as needed to fill radiator. Tiny to no bubbles should be seen at idle after 20 minutes for successful bleed.
4) after bleed let engine cool completely then too add radiator and reservoir to proper levels.
Failing/failed water-pump is also a possibility.

If you have already replaced the thermostat or you don't think think the thermostat is the issue then set the interior climate control to max and fan on high. From a cold start let idle with the radiator cap off. When the thermostat gets hot enough to open rev the engine slightly while looking into the readiator from above (keep your face as far away as and wear safety glasses when looking into the radiator from above it).
At idle you won't see much current flow in the radiator, but when you rev the engine there should be swift flow in one direction. If there is no flow or weak flow while revving then replace the water-pump.

As Chez and Colin replied if there's a loss of coolant in the radiator combined with excessive or overflow in the reservoir then it points to a breached head gasket. If this is the case start by purchasing a new Honda Genuine radiator cap. A failed rad-cap can cause the same symptom.
Doing a block test is also a good place to start when a head gasket breach is suspected If a block test is positive (blue test flud turns yellow or green) then it's proof unwanted emission gases are entering the coolant through a head gasket breach.
However, if the block test is negative it doesn't rule out a breach.
Best test for breach is similar to a leak down test but without the leak down tester attached. Use straight shop (compressed) air at 150 psi, rad cap removed, inject air into cylinder with piston at TDC and listen and look for air bubbles coming from radiator beach. Test all four cylinders individually this way.

Read the link about the types of head gasket breaches below in my signature.