I have a 2005 honda civic ex 5 speed and the rpm idle up and down while its doing that the battery light comes on then its stops and the check engine light comes on. tried to scan it but it read error

SOURCE: 1991 Honda Civic 1500 idles irregularly, with check engine light.

I think I would suspect the fuel injectors, especially since that is the code you are getting. Fuel injectors clog up, get dirty, stop working the way they should. They can be cleaned (you can remove them and send them to a company that cleans them and makes them like new, or, they can be cleaned in the car by some garages, or, you can get a can of Sea Foam spray and spray it into your throttle housing several times to try to do some cleaning that way, or, you can dump a can of Sea Foam (non-spray) into your gas tank and run it with the fuel through your injectors). You should probably check when you first start the car to see if you are getting any leakage from one or another injector (one or another may look moist or wet if the seals are leaking). You can also do the long screwdriver test (hold the bit of the screwdriver against each injector in turn and listen with your ear against the other end to see if each is clicking regularly). I would try the Sea Foam first.
I hope this is helpful in getting you started on a fix.

Testimonial: "Quick response and good suggestions. I have not yet verified the solution but believe that I'm troubleshooting in the right direction."

SOURCE: HONDA CIVIC 1996 PULSING IDLE

It might be bad gas or a plugged filter or it might be a bad mass airflow sensor.

SOURCE: honda civic ek3 1999 model

I assume you mean low idle speed 500 rpm. Genarally a tapping noise comes from the valve train, and a knocking noise comes from the crankshaft connecting rods. The way that a mechanic will narrow it down is to use a mechanics stethoscope. You can get one pretty cheaply at an auto parts store. Put the metal end of the scope on a part of the engine and listen for noise. On the other hand, if your car is idling at 5000 rpm, it would also be making ALOT of noise.

SOURCE: check engine reads P0740 honda civic

I am sorry to bum you guys out, but this usually means the piston in the torque converter is bad. The converter needs to be replaced along with a transmission flush.

SOURCE: problems wont pass 4000 rpm's

Depending on the model of accord. It may be a VTEC malfunction in the computer. If it's an EX it is a VTEC