I am doing a custom restore job to 79-80 CJ. the body was lifted 3" and a 2 1/2" BDS lift. Any thoughts about whether I should lift the whole drivetrain also? I like the idea for a flatter underside w/ more clearance.

if you raise it too high you will have a terribly high center of gravity. but raising it a little work be great. make sure your driveshafts still work you might need a cv or double ujoint shaft.  

it's probably a bad idea because of the driveline angles. even if you use  a double cardan joint, you may have to grind it so it doesn't bind. that just doesn't seem natural.