I read through it and the authors seem to seperate the issues one is the clunk the other is the shifter coming out of gear.
That's because there are two different scenarios that can cause the clunk - one is the front diff and the other is the transfer case - the front diff clunk is caused by the air operated SOTF diff clutch jumping a tooth - and the transfer case clunk is caused by the engagement dogs jumping a tooth. IF the transfer case is in 4H it will jump back to 2H, if it's in 4L it can't.
You've already replaced the front 3rd member - presumably you no longer have the air operated SOTF diff clutch - if that is correct, then you're most likely getting the noise from the transfer case. If, on the other hand, you still have the air operated SOTF setup, then, you may still be getting the clunk from the diff.
Is the TC chain driven? Does it have a clutch or something in it designed to slip?
Yes the TC does have a chain, it drives the front output shaft, and as far as I'm aware, no there is nothing inside designed to slip.