tranny rebuild- ADVANCED AUTO

Im having my tranny rebuilt courtisy of ADVANCED AUTO, They sent me the wrong axles and i even double checked them, so now my tranny is all messed up, but there paying for the rebuild…anyhow my question is what are my avalible choices for gear sets, or is there a mix match type deal w/ gears??? I figured i would have them install the gears so its no big deal…any ideas comments are welcome thanks guys