Electrical issues

ok so here it goes....I bought a 2002 fz1 after it had been laid down. Now the bike was running and driving when I bought it. About 2 weeks later after I had put new oils and tires I spun a rod, so yesterday I transplanted a 05 fz1 engine in and got it running same day. Now here the kicker. The previous owner had rigged up some bs headlights with zip ties and had 2 toggle switches to start. (I left one functional switch while swapping.) I put a street fight front fairing and headlight on it and got to messing around and noticed how much wiring had been changed around. Well I had my bike at my shop and needed to get it home so I ran it without the fan because I wanted to put a relay for it so I figured if I didn't run it hard it would aircool as I wasn't drive to greater distance. Well coming into town I lost all power to bike. No lights no nothing. That is the jist of it. Any feed back to what I can look for. I dont know much about bikes but am a decent mechanic
 
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