Gentlemen,
I too just went through this dilemma. I used the Bilstein website application chart, Shock Warehouse application chart, and made calls to Sean Lorenz and Off Road Warehouse.
It seems the 2nd gen shocks can be used on 3rd gen trucks. However, the spring rates are different between the 2nd and 3rd gen trucks, thereby requiring shocks to be valved according to application. Too, if you have added more lift over factory equipped, then it changes the shock needed as well.
That said, betterthanstock, you've referenced Bilstein numbers I have yet to hear of, or have seen on any 5100 series application charts. New re-valved 5100 series shocks... possibly? By the way, the only charts I've looked at are for the 5100 series shocks, therefore may be Bilstein's heavy duty series (yellow shock, blue boot).
BClevenger,
According to the application charts I'm looking at right now, the BE5-6681-H5 (front) is used on 94-02 Dodge 2500 trucks with 2" lift, and 03-06 Dodge 2500 trucks with 0-2" lift. The BE5-6682-H5 (rear) is used on 94-02 Dodge 2500 trucks with 0-1" lift. The 6682 is used on the 2nd gen trucks because it's valved for the spring rate of that rear leaf. The length of the rear spring changed (longer) on the 3rd gen trucks, therefore so did the spring rate.
Will the 6682 work on the 3rd gen? Sure, but not optimal for the application. If you're planning on installing the 6682 on a 3rd gen truck, don't. Send the shocks back for a refund and order the BE5-6647-H1 (rear) from Sean Lorenz or ORW. The 6647-H1 is made for the 03-06 trucks with no lift other than factory.
Hope this info helps. I had to ask a lot of questions before getting the answers I was looking for too. Take care.
Dwayne