Springs arent supposed to bend much in the middle. if ya can see the whole rear end twist from the springs flexing id replace them..... Stock XJ springs suck pretty bad and sag easily.
the HD springs from quadratec give 2" of lift...... a set of 2 inch spacers on the stock coils in the front will even it up nicely and your ride quality will still be good.

 

So the OE HD springs ad 2" lift? This is what I have been trying to confirm before ordering. Do you have before and after install pics by any chance?

 

My vote is motor mount(s). Second would be trans. mount.
I have this issue too, (along with some other, related, I think), noises/vibes from a standing start. Although, I wouldn't be surprised to learn it has to do with weak leafs/axle wrap in some cases.

 

I know noise and vibrations can be easily transferred thru the frame to feel like it's coming from somewhere it's not, but it REALLY feels like it's coming from the aft end...u-joint(s), hung drum brakes, soft springs, etc...I hope to figure this out this weekend. I don't think it's hurting anything, but it also isn't going to get better on it's own.

 

I don't have a thud from a stop, but mine has a hell of a clunk where the whole truck moves when going from reverse to drive. SO... Today I got the wife to go from park to reverse to drive and back and forth while I watched the whole drivetrain. I have some serious axle wrap going on. I watched the rear diff move up and down about 1/2- 1 inch, possibly more as she went from R to D..... The U joints are all tight. No play in the T case. i have original leafs, they seem pretty worn.

 

Your drum brakes time to service them.

 

Even if the springs flexed a good bit? Not much arch left, pretty flat.

 

Same thing here...I had a buddy of mine who is a Master auto tech at the Bimmer shop under mine when I did the same thing. Lots of movement, but he wasn't concerned. Biggest thing he said to do, IF I wanted to, was to change the leaf's. One of these days...