KA and 5 speed swap going bad

[silvia180SX]

I have an 89 240SX that was previously and automatic. I put the drive train out of a 91 Hicas edition car into the 89. The swap went OK and all the 5 speed stuff is mounted but the wiring is problematic. I looped the female blade connections like I was instructed to by the swap pages but the car wouldn't start and when I pulled the fuse box cover the ALT 75 Amp fuse was blown. I replaced it and put the neg battery terminal back on and it blew again. When I bridge the fuse and touch the neg terminal it sparks and the battery almost blows up. It does this when I use the auto (pos battery/starter/alternator) wiring and the 91's wiring as well. How can the wiring be that screwed up, both harnesses came out of a 240???? Is there something to a 5 speed AND KA24DE swap that I am missing??