Problems with wiring???

I am not sure what to make of this problem I'm having. My parents have a 92 stanza that they thought had a bad alternator so they replaced it when they did they found a weird wiring situation were it lloks like the previous owners had done some inventive wiring. When they put a new one in they hooked it up in the regular way. When they went to connect the battery it apparently sparked really badly. The car won't start and the power windows and radio are out and the headlights are a little dim. I tried tracing the wiring back from the battery looking for a fault in the wiring. I replaced one piece right next to the battery (a short blue wire with connectors on both ends) this fixed the power windows and radio. The car still won't start it acts like it wants to but just is'nt getting enough power. I have checked every fuse and a substantial amount of the wiring. I don't know if it was the spark when they connected the battery or the wiring job on the alternator or if the alternator was never bad to begin with and it's something else entirely. So if any of you have any idea what it might be I would really appreciate the help.
Thanks