I've got a non-intercooled 12V project in the works and managed to squeeze it in without any lift. It took me 2 tries as I originally wanted a crossmember near the motor mounts but realized this was impossible without a lift. It is close, but preliminary flexing looks like it will work. I have not given up on the crossmember idea yet. I also have the getrag so I swapped out the stock np200 yolks for 1410's (thanks Mikel). You are going to have to fab your drivelines, that is a given, so you might as well get your transfer case mounted where you want it. The transfer case has proven to be the most difficult part of my project so far because of all the angles that are supposed to be just right.
I would like to see some pics of your project!