I'm starting here because to me this is the swap that makes the most sense for a rock-crawling machine and is probably the least explored. As you'll figure out shortly, I'm pretty opinionated on this one and I welcome anyone to dispute my views. I believe that diesel engines are superior to gas ones for offroad use for many reasons. They tend to make usable torque at much lower engine speed than gas engines. This means you don't need nearly as low a crawl gear. They also feature a much flatter torque curve. There is no ignition system to fail because of moisture. They are not as affected by altitude, in fact, turbocharged diesels are virtually immune to altitude. In most cases, even though they have all the advantages of a fuel injected engine, such as the ability to run at extreme angles, they rely on mechanical injection which is considerably simpler than electonic injection. Diesel engines also tend to get much better fuel economy and greater cruising range than gas engines of similar displacement.
There are three commonly available engines that are suitable for swapping into Land Cruisers. Probably the biggest obstacle to the conversion is finding the engine itself. The GM engines are the only ones listed here that are available in light-duty automotive applications. The others are all industrial/medium duty truck engines. These motors tend to be snapped up as soon as the vehicle they were in is wrecked and rebuilt by companies with exclusive licenses. Unless you're willing to pay top dollar for a rebuilt unit (not a bad idea) you have to somehow find a way to intercept a motor before the rebuilders get their hands on it.
The most easily obtained is the GM 6.2l diesel. A conversion kit is available from Mark's Adapters in Australia to mate a GM diesel to a Land Cruiser 4 speed manual or automatic transmission. The GM V8 supposedly weighs about as much as a big block, so pretty close to the weight of a 2F. The L65 is found in C/K 2500HD trucks, C/K 3500 trucks and C/K 2500 Suburbans. The L56 is found in C/K 1500 trucks. C/K 2500 LD Trucks, K1500 Blazers/Tahoes/Yukons, and C/K 1500 Suburbans. The 6.2l is found in all pickups and Suburbans, and in Chev/GMC P30/P3500 step vans.
The 8th digit in the VIN of the donor vehicle indicates the motor type:
The GM 5.7l is without a doubt the worst diesel engine ever cobbled together. It is the Olds 350 gas block that was converted to diesel. Probably 99% of these motors have been blown apart for at least 10 years, but some may still be kicking around. If someone offers you one, they are NOT your friend.
A slightly more rare engine that I see as being a better match to a Land Cruiser is a Cummins B3.9 litre turbo diesel. It was used in among other things, Ford E350 cube vans, and Case 580 Tractors.
PowerMark used to offer a conversion kit (p/n RK9525G) that was designed to allow you to bolt in a B3.5/5.9 in place of a GM 292 I6 or 350 V8 in GMC cube vans. In order to put this engine into a LC using the stock transmission, you would simply need to get the motor mounts/bellhousing Advance Adapters sells for putting a V8 in and use the Cummins engine instead, as well as possibly having to modify the supplied intake system and radiator hoses. Unfortunately, PowerMark has now gone out of business. Fleet Supply has bought up the remainder of their stock and plans to continue production. They also plan to introduce a kit for Chev/Ford pickups. The kits should be available from your friendly neighbourhood Cummins dealer.
I think the Cummins B5.9, as used in Dodge Ram is definitely too heavy to put into a 40 series, and is a little heavy for a 55/60/80 series. It is also a little on the long side. The above mentioned kit would also work for a B5.9.
The best diesel swap into an FJ40 I've ever seen is the Isuzu 3.9l diesel, model number 4BD1T. Two of its applications were in Isuzu NPR series cab-forward trucks, and LINK-BELT LS2700CII (4BDIT). I also believe it was used in the GM Forward 3000-4000 series trucks. There are two paths for putting an Isuzu diesel into a Land Cruiser. The first involves a factory Isuzu adapter bellhousing. It is designed to mate any SAE #3 flywheel cover to a GM manual transmission with a 5.125" bore (SM420). The bellhousing bears the casting number WF 150015. Unfortunately, this bellhousing has recently been discontinued. There are still some around--try your local Isuzu dealer. A better option is an adapter ring. I have yet to locate a commercial source for these--the one I've seen was made years back by a company that has since gone out of business. The ring allows a GM bellhousing with a 350 bolt pattern to be attached to an SAE #3 flywheel cover. Using the adapter ring, it would be possible to attach the 4BD1T directly to a Toyota transmission with an Advance adapter Chev->Toyota bellhousing.