Assuming you set the gears up properly, the vibration could be coming from U joint angles. I would check there first. Remember that with the 4.56 gears, the drive shaft is turning faster. If you put a vehicle up on jackstands and run it in gear, yes, you will hear some scary noises. I did that to mine not long after changing axles and gears . What you're hearing is alll the back lash in gears- transmission, transfer case, rearend gears, axle splines, etc. because the drive train is unloaded. The sounds will be worse if you have a slightly warped brake drum as it will tend to load and unload the drive train as it turns.
If you suspect gears, listen for changes in sounds going drive to coast in 4th gear. There should not be a significant change. Improperly set gears will make a whining or growling sound usually on coast conditions when you release the gas. Several years ago my friend had new gears installed in his 83 J10 truck. about 10K miles later he asked me to install a Detroit in the rearend. Before pulling things apart, I measured the backlash, It was at .013 or so. I am assuming the shop that set the gears had set it in the factory range (.007-.010) on setup. When he sold the truck last year, it was still running quietly (the gears, the Detroit had it's usual clunks and bangs).
Yes, pinion preload will loosen but how much, I don't know. Just make sure you can't shake it up and down/in and out. I set up 4.56's in a friends YJ a few years ago. Two years later, he wanted to change to 4.88's which I did for him again. There was less than 4000 miles on the Jeep since installation of the 4.56's. I was surprised at how easy it was to turn the pinion. It was like it had lost a lot it's preload but everything turned smoothly with no slop or play.
Last edited by 80cj; 02-07-2010 at 02:38 AM.