I'm in the process of an LS swap right now, and due to having surgery on both hips 40 years ago and 4 low back surgeries my wife talked me into going with an automatic transmission so I can enjoy driving it more and not be clutching & shifting, especially in stop and go traffic, which might become painful. Here in Florida I was able to get a good Gen 3 LS for $800 with everything on it including A/C (and they flashed the ECU using my differentials ratio, tire size and so on), and the 4L60E automatic overdrive transmission for $700, and a custom made wire harness for $200. Hopefully that gives you an idea of costs compared to doing a 350 and then fuel injecting it. You may be able to find them cheaper in your area. Oh, and then there is the cost of the motor mounts and Advanced Adapter to connect the transmission to the transfer case, and you would want to run a split transfer case instead of the original or I'm told the transfer case would whine so bad it would drive you nuts.
Cruisermatt owns and operates a shop near Orlando that works on Land Cruisers and when I was over there he said the best driving & riding FJ40 they have ever done was one they did an LS swap on. He said it felt and drove like a modern vehicle, and that it also takes 300 pounds off the nose because the LS setup weighs so much less.