pics would help out a lot with this! i know you said you gona post pic later...
does the big red wire look like...
that? really flexible and see through vinyl skin? then it probably was for a stereo subwoofer amp.
and the wire in the trunk...does it look like a stock wire coding?
i'll wait for the pics.
and if you have a volt meter..put it to a DCv 20V setting, put it to the battery terminal with car off. normal batt should read 12.4~9v's, and with the car on, the alternator should be feeding the battery with 13.9~14.9V's.
edit: you said you use the black/decker charger right? does it give you battery voltage reading when you hit the button that says "Voltage check"? if so..hit that button while it's connected with the car running and see how much volts reading it gives you.