Electrical help needed

Last month I went on vacation for 3 weeks, during this time it rained like heck on my civic. When I returned from vacation, I started my Civic and
immediately got a "Charge System" light, and "ABS" light and a "SRS" light.
The next day the car wouldn't start. I pulled out the battery and it wouldn't charge with an automatic charger. I thought that the problem was the battery (6 years old) and I went ahead and replaced it. I placed in the new battery and now whenever I connect the battery the following fuses burn instantaneously and the car wont start (it'll turn over but I don't hear the fuel being injected prior to the starter and I don't detect any smell of gasoline):
Underhood Fuse Relay Box: Fuse # 44, PGM FI main relay Fuse #47, Audio Unit Fuse #51, Door Lock
Underhoos ABS Relay Box: Fuse #62, ABS Control Unit
Under Dash fuse Relay Box: Fuse #15, Alternator SP Sensor, ELD unit
The car is a 2000 Civic Coupe SE, D16y7 with ABS brakes.
I've tried: Replacing the fuses Disconnecting the alternator The whole to no avail.
I'd greatly appreciate any help you can give me. I would tow the car to the nearest dealer but it's going to cost me a small fortune (over 40 kilometers away).
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EDSD wrote:

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I hate to bring up the most obvious question, but is there any possibility you installed the first or second battery with the red wire on the black terminal? (some batteries have the terminals on the 'wrong' side)
It sounds like you've fried the diodes in the alternator as well as other stuff.
'Curly'
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I hate to say it, but that was my first thought too. It is also possible for aftermarket battery wiring to be the wrong color! The only sure way is to look on the battery for the polarity markings molded into the case near the posts; a "+" and a "-" usually in circles, and follow the "-" wire to the engine block or the body of the car.
If the wires are reversed, the way to test it is to correct the wiring, replace the blown fuses and see what works and what doesn't. Especially check to see if the system is charging - check for at least 13.6 volts DC and less than 0.1 volts AC across the battery with the engine running. If the voltage is at least 13.6 DC, make sure it is inder 15.5 volts DC (warmer temperatures give lower readings) or the battery will be ruined within half an hour.
Mike
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I believe this car uses a post type battery which has a large and a small post. This is a way to fool proof this type of error. This should be obvious to the battery installer.

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Burt wrote:

Thanks for all of the replies,
I am usually a very careful person and will check and double check things before installing, I am certain that the battery was placed in its proper form, in fact, I've taken a voltmeter just to be sure. Last weekend was the first time I had a bit of time to look over the car, this is what I found:
the following fuses continously burn: Underhood Fuse Relay Box: Fuse # 44, PGM FI main relay Fuse #47, Audio Unit Fuse #51, Door Lock
Underhoos ABS Relay Box: Fuse #62, ABS Control Unit
Under Dash fuse Relay Box: Fuse #15, Alternator SP Sensor, ELD unit
The car beeps 6 times whenever I insert the key.
The following systems work: headlights parking lights horn brake lights emergency lights wipers the A/C fan comes on the interior dome light starter motor
The following systems do not work: Radio Door locks aftermarket car alarm (with fuel pump cut-off) I still do not hear the fuel pump engage for the 2 seconds after I insert the key into the ignition. The automatic transmission will not shift out of PARKING
I used a self-powered light test (actually it beeps) and fuse #51 (underhood fuse relay box "keyless door lock") makes contact with both ground, on one side, and positive, on the other. I traced back the origins and by removing the car alarm (disconnecting the harnesses) I found that the fuse would no longer go to ground but all the other fuses still burn.
So far I have disconnected all of the harnesses in sight, including under the dash, the abs, keyless door lock and in the engine compartment, I have cleaned and left them to dry for several days, the whole to no avail.
I know that somehow everything is probably connected to either a bad ground or a bad wire, the problem is that the wiring diagrams in the "Chilton" manual are not specific enough.
Any of your comments and recommendations would be greatly appreciated and if I do find the problem, I will happily post a very detailed message to the benefit of other people who might experience a similar problem.
One last note, for the past two years my fuel gauge has been erratic, out of the blue and while at a red light, it will stop reading the amount of fuel in the tank. Five minutes later, everything will be ok. This happened perhaps 6 times in the past year or so.
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This sounds like a short that has melted its wire to several other wires. Logic will tells me to disconnect the alternator, disconnect the main relay and jump battery power to the fuel and ignition system so you can drive to where ever you want. Make sure you connect the jumper wire with a fuse (say, 15-Amps) attached.
The way the PGM FI fuse blows tells me that Honda doesn't care if you get stranded just because other circuits failures.
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