I'm currently in the process of collecting all the stuff to drop a 3B into an FJ55. I decided on the 3B primarily because I have two other trucks running them right now so I have a reference if something doesn't work right off which is bound to happen. I've found a complete wiring harness from a wrecked BJ60 which will become the basis of the wiring from the dash forward. The deisel ignition is totally different from the gas engine and will require an entire rewiring if you want it to work with some automation and with the safeties in place. For instance when you start the truck prior to cranking you need to preheat it, either through glow plugs or an intake air heater (different ignition switch and glow relay/control), the initial mixture is usually richer than normal so you need to overinject (EDIC motor or manual pull), to shut down you need to remove the fuel source (deisel does not need power once it runs if it has a mechanical injection pump) so you need the EDIC or the manual pull. The 3B and I assume the other Toyota deisels have a low oil pressure cutoff (inoperable without some form of automation, either through the EDIC or a solenoid valve).
As you can see the engine operation is significantly different that that of a gas engine.
There is another user on the board who is in the final stages of a deisel into an FJ60. You may want to PM him if you're serious about this and find out what his pitfalls are.
A deisel to deisel swap is not a big deal like a gas to deisel swap.
A deisel swap will affect your A/C as the amplifier is different (no coil feed) the tach is different (again no coil feed) and I'm sure there is a ton of other issues that I have not even thought of.
The benefits are huge as far as I'm concerned. Things like double the fuel mileage, loads of low end torque, great durability and reliability.
It's a
job though!