"When rounding up parts for your conversion keep in mind that '96 and up motors are OBDII and will not be smog legal for California.
From a Sidekick or Tracker:
You will need the engine complete with all of the hoses, pulleys intact. You will need the fan, starter, alternator, coil, air cleaner, exhaust manifold, head pipe, engine room wiring harness, under dash wiring harness, ECM, and speedometer.
In addition to this donor parts list you will also need a high pressure fuel pump, an engine adaptor kit, and slightly taller mounts or shims for the front 4 body mounts in order to provide for hood clearance. The donor vehicles wiring harness will need to be modified for use in the Samurai as well as the Samurai speedometer which will need the speed sensor from the donor vehicle adapted to it."
I had copied the above information from a post. This is not my info, but it does come from Trail Tough.
You will need the entire engine bay wiring harness and the entire under dash wiring from the donor vehicle. When you have it modified, you install it in conjunction with the Samurai wiring harness. The Samurai harness will be left in the vehicle, you will just be adding to it.
Just a thought, maybe you could come up with an entire donor vehicle. Keep and use what you want. Sell the leftovers and try and get some of your money back. That's what I did.
On the fuel pump, TT's inline pump was a noisy son-of-a-gun. I tried to quiet it down, but didn't have any luck. I ended up using a Samurai EFI tank and pump. It is nice and quiet now.
Good luck with the swap. It is definately worth it.