@theaviator When you get into an FJ40 project, the good thing is that you have a whole range of setups that you can go for, but all this depends on what your primary purpose for the vehicle is. Whether its offroading, rally racing or touring will help you to define the kind of machine you want to build. I have used a many different engines since I got into this hobby. The first was a 1KZ-turbo(86' RR), auto tranny, which I loved. Followed by a 3B (87' BJ60) which had a 4 speed tranny, gave great mileage and good torque, then came the TD42 (90' NP), that was a beast of a heart on my Nissan Patrol. Then came the 1HD-Turbo(90' 80 Series), manual tranny and that was by far the best I've used so far. Now I am using a 1FZ-FE (92' 80 Series), auto tranny which will make you happy once you put your foot down on the pedal but by default I think all of us drivers have a inbuilt sensor in our brains that keeps our eyes fixated on the fuel gauge 
I have 2 suggestions for you.
One would be to keep the 2F and run it stock, keep it tuned well and get a 5-speed tranny for it.
The second option would be to go for a good, strong and reliable diesel engine. You already have the experience of a 1KZ and its definitely an option to consider. Its a great engine. All this depends on your budget. Even if you get a 3B (3400cc) with a 5-speed tranny, it will be really good on diesel consumption and the 3B has always been regarded as a 'bulletproof' engine.
These are just my thoughts from the experiences I have gained so far.
Do keep us updated and good luck.
