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).