well, you don't really need any harnesses except the one actually on the engine (that has injectors plugs, and big bale connections) and the one that goes from it to the under hood fuse block. I'm not real sure about what all can be deleted from these but it's a fair amount. It doesn't take but a few fuses and relays (about 5 wires if I understand right). I know you'll need power, ground, starter wire, OBD II plug, wiring to throttle pedal.
There's a video on youtube of a guy doing a walk through of exactly what is needed for a dmax to run. He goes through it with a dmax on a engine stand.
If you want the factory gauge cluster, it becomes a good bit more wiring as that is ran through the body control module of the truck. IDK what all else what would/could be deleted from that if it's not used for the cluster. It's not nearly as tunable as the ECM with the likes of EFI Live. I think you could do what you needed with it with a Tech II module though if you can get access to one of those.
Good luck.