Yes you can run a standalone ECU, and that's probably the simplest option is you can afford it. It also gives you maximum flexibility for future mods, and you don't have to worry about stuff like factory boost cut.
The 2JZ engine harness is nothing like the 5M harness. The 5M is basically a discrete bunch of wires which goes between the ECU and the engine, so you just add 12 volts and it runs. The 2JZ is a completely different kettle of fish as the engine harness is integrated with just about everything else. To give you some idea, when I pulled my front cut apart I found 11 computer modules attached to the harness, and I had to remove all but one. That involved tracing hundreds of wires to find out what went where - a rather time-consuming task!
You could just throw the entire harness in the car and leave the excess stuff dangling, but the excess wiring I stripped from my harness was enough to fill the back of my Supra...