I currently am running this set-up (4.6 crank & rods with 4.0 pistons) and have done so for the last few years. I have a 96 GEMs disco running 4.6 crank 4.6 rods with 4.0 pistons installed on the 4.6 rods. You gain compression up to about 10.9 : 1. I am also running a 4.6 cam and using my old 4.0 heads, intake etc.
I noticed a nice gain in both torque and power. Enough that I really like this set-up. I've been told by others that if I were to put a chip in the GEMs computer I'd see even more gains but frankly I like what I have. It is much better than a 4.0 - a very nice upgrade.
I will share as to not over sell this, good friend has a stock 4.6 Bosh in a similarly outfitted disco II and I think the stock Bosh 4.6 still might have an edge on what I have (maybe the bosh injector system or computer?) BUT the change was such an improvement from the old 4.0 I feel good about telling folks it is worth doing - - I am not sure I would have needed the 4:10's if I had this motor first.
I DO think a chip would give more power to the truck but I do not have any knocking or pinging problems and it performs well much better than it did prior without a chip added. Looking into a chip it looked expensive so I have not gotten there yet. The engine has also held together nicely - - even though the first weekend it was in the limiter multiple times.
Others have it correct you cannot nun 4.0 rods on a 4.6 crank as you will hit the heads - the 4.0 & 4.6 pistons are the same height from the wrist pin to the top of the piston the difference is in the dish size of the pistons - the 4.6 has a larger dish thus why lesser of a dish of the 4.0 piston gives you more compression.
Assume you have to use premium high octane fuel? Really old post so if anyone else wants to chime in, please do.