I just did a test fit on my 1969 FJ40 today using the F engine originally in the truck and an H42 and split transfer case from a 1987 HJ60. I am using the early 2F bell housing as well to take advantage of the rear motor mounts, but I don't seem to have the same issue you are experiencing? I am trying to figure out why. Maybe we can compare notes? I am trying to decide between rebuilding the old F engine or putting in a 2F from a 78 FJ45...which is where the bell housing I am using came from.
Here is a photo of my setup in place.
Here is a photo of my setup in place.