I don't know about the other engines you mentioned, but 1KZTE gives an average of not more than 6/7 km/ ltr. Go for the original 3L. An amazing machine. Around 12/ 13 km/ ltr average if run below 100km/ ltr. Non efi, non turbo, no wiring, get a 5 speed trany with it and enjoy life. A 3L has also come in 5 door prado so no issues of power. And getting it overhauled will not take you more than 4 days, not a big deal.
My personal experience is that one must think 10 times before changing/ fixing different engine other than the stock. And than being new in restoring, you must try to avoid alterations and electrical hassles.
Remember, "pakistani bivi aor efi engine kay masalay kabhi khatam nahin hotay".