The answer to your question depends on some variables.
For example: What is your budget for this engine swap? What will you use your FJ40 for primarily? Offroading or daily driver?
If diesel is the way you want to go, then there are many options. You can go for a 2B or 3B, both are reliable and good fuel average giving engines. Plus whenever you will need the torque, it will be there waiting for you.
As far as fuel prices are concerned, yes maintaining a diesel engine might be more expensive in terms of oil changes etc, but diesel will always give you more kilometers on the clock as opposed to petrol.
You might want to check the 4x4 Loot Sale thread, might be something there for you or someone who will be able to help you out.
Good luck.