So the most difficult part of the conversion is certainly the wiring. However, there are guys in Australia that can help you out. They'll even build complete harnesses for you so it's plug and play. I'm currently working that out as I decided not to modify the dash harness myself...
As for the immobilizer, fun fact, early model HDJ101's, 98, 99 and I think 00 do not have an immobilizer from factory. My ECU is from a 99 HDJ101 and it checked out. So I would say keep an eye out for early model HDJ101 donor vehicles for your conversion. Also, as I understand, it's better to use an auto ECU as it will have cruise control as the manuals do not.
Also, stick with going with an FTE for your conversion. Yes, it's more of a hassle to get running, but it is the superior choice of the bunch. Keep it stock with a 3" exhaust and it'll go forever.