Complete wiring harness replacement help

I recently traded for a 95 Nissan Pathfinder 4x4, the wiring harness had been chewed by rats but the previous owner already had the replacement wiring harness to be installed. I didn't realize until after I started wiring it in that the harnesses weren't exactly the same so now I have left over wires that I'm not sure where they go. I've looked at diagram after diagram and I'm still lost on the best way to proceed. Any help is appreciated because I'm at my wits end. Thanks in advance