Hi,
I still haven't tried the SETRAN method, because right now I'm trying to substructure a system using the top-down method (because the full system, meshed, fits in memory; it's only too heavy to perform a transient analysis with), not the bottom-up method as in your case.
I believe that, when defining the superelement, ALL its nodes must be rotated to the same ESYS. This makes sense if we think about the meaning of "superelement": it's a matrix whose coefficients must be referred to an element coordinate system, but if some nodes of the substructured part are rotated in different coord sys, there can be mismatches or unpredicted results.
Remember that SETRAN only creates the new superelement by re-attributing it to a new ESYS, or by adding an offset matrix transformation to the superelement matrix, or both. You still have to use SE to read it in the use pass.
If you find that the new superelement is not in the position you expected it to be, probably you missed the offset transformation. In fact, I suppose that the coord sys reattribution is just like when you EMODIF some elements to have a new ESYS, but it doesn't shift the node locations; in addition, setting SETRAN's NOROT key to 0 seems like issueing a NROTAT,all in the new coord sys for all the nodes of the superelement (that's why the superelement matrices are unchanged). Only suppositions, though, as I haven't tried it yet (and supposedly won't try it for a while !... ;-) since I still have to finish my investigations on the top-down substructuring... I'm a beginner in that field...)
Hope this helps in some way.
Regards