When you say SJ T-Case, do you mean an SJ-410 or a SJ-413?
The SJ-410 is 10% lower in high and low range then a SJ-413/Samurai T-Case. Other then that they are pretty much the same. I do know that aftermarket gears are not supported in the 410 case, so some of the internals might be different sized.
As for the flanges, they are probably the same. I didn't check the top flange when I swapped over to a Sammy case, but I know the rear E-Brake flange will bolt straight up to a Samurai/413 case so chances are the top flange is the same.
The bolt up positions are the same for both T-Cases.