If you have the original 3.07 differential (wider) and homokinetic axles, the replacement axle is shorter.
I've converted mine to a 2.47 differential (narrow) and installed annular axles, which are longer. The advantage to this is lower rpm's at cruising speed (quieter), slightly better fuel mileage, and ease of repair (replaceable cv joints/boots).
Some have used the 2.88 differential (used on the 85) because of better off-the-line performance. However, they are more rare. Also, I'm not sure about the width of the 2.88 differential.
I gleaned a lot of information from here:
http://www.peachparts.com/shopforum/diesel-discussion/249673-2-47-1-2-88-1-axle-116-120-a.html