I found the problem. It's actually the crank sensor itself. I put a new one and it did not burn the fuse. We havent' put the whole timing covers together so we do not know if it really works but we are pretty confident that that's what it was. It's been cold here lately and maybe in another month or so. Thanks for those who replied.

 

Put the timing covers on and everything back on and unit ran with no error codes. I think moisture got in there somehow and shorted the pins. This can happen again so I taped the connection with an electric tape. Thanks again fro everyone's help.

 

Its the crankshaft sensor i have a 2001 civic vtec and had the same problem the sensor falls apart and the insides fall out and ground out against the harmonic balancer, disconnect the crankshaft sensor replace the fuse and turn on the key to see if the fuse blows out, this happened to me twice on the same car good luck guys

 

I know this is an old thread, but it just helped me diagnose my problem with my 2003 Honda Civic! Thanks for the help! Details below:

My car stalled while driving down the highway. Would crank, but wouldn't start. Towed it to shady service center. They found the #6 F1 ECU fuse kept blowing, but couldn't figure out why. They talked about the fuel pump etc - had no clue. So I did a search and ended up here! After reading some people had problems with their Crank Shaft Sensor, I unplugged that and voila! The fuse didn't blow any more and the engine would run! I got the hell out of there since they didn't know crap and limped my car home. Took it back to the dealer that had replaced the Crank Shaft Sensor 11 months earlier (a month after they changed my timing belt and water pump, the Crank Shaft Sensor died... coincidence??) and they found corrosion in the plug and replaced it for free.

Long story short:
dealer replaced timing belt and water pump.
1 month later, Crank Shaft Sensor went bad.
Dealer replaced that.
11 months later, car stalled and wouldn't start (#6 fuse F1 ECU kept blowing)
Ended up being corroded Crank Shaft Sensor plug.
Spliced in new plug... good to go!