I can get you all the measurements you want of my 4BTA/4L80e/Split Case in my 1964 FJ45. 
I can also get you the measurements of the 700R4/Split case combo sitting here in the FJ55.

I can also get you the measurements of the 700R4/Split case combo sitting here in the FJ55.
yeah,
What i would want to know is the total distance between the engine mounting surface to the transfercase mounting surface on the 4l80e. Also, whats the width of the bottom oil pan on the 4l80e, and how that relates to the distance between the frame rails in that location.
I was just talking to Jason earlier today and he says he met a guy that had a LS1 with a 4L80e in a short bed FJ45. I don't know how long the driveshaft was, but I know that the stock wheelbase of a short bed FJ45 is 10" longer than a FJ40.
How far back did you move your rear axle?