I have a 01 4runner sport with a bull crap rough country lift and it doesn't sit level due to compressed front coil springs. Im going to put coil overs in it to level it back out and get rid of spacers in the front but I've noticed they all say you can't go over 2" if you have auto locking hubs. So the question is do they since you obviously don't have to lock them..? or is it something completely different that locks your cv's in? Nothing i have found can give me a yes or no.

 

3rd gen 4Runner had what Toyota called ADD...automatic differential disconnect. The front hubs are always locked to the CV axles. The CVs rotate as you drive. The CVs are disconnected internally at the front diff. Only thing that matters is how much of an angle you are willing to tolerate on the CV axles between the diff/diff tube and the wheels. 2" lift is considered safe...no mods should be necessary. More than 3" and the CV axles ride at too steep an angle and fail much faster.
My '97 got lifted about 2.5" initially in the front, before the inevitable sag-down, and there have been no issues with the CV axles or CV boots in 20K miles. i prefer that the rear be a touch higher than the front, 'cause I hate when I load it with gear and then the butt drags low.

 

for the N185 (1996-2002 4Runner), it is ok to have 3" of suspension left as long as you install 1" front differential drop to reduce stress on the CVs and also to lessen the possibility of torn CV boots. The front diff drop is needed if you go for more than 2" of suspension lift.

Also, for 3" of lift, you will need to install an aftermarket Upper Control Arm (UCA) for the front to be able to get a correct alignment of the front wheels. One of the better UCAs is SPC Performance UCA (this is for the Tacoma, but will also fit the 1996-2002 4Runner):

http://www.spcalignment.com/componen...AFrom&to=USATo

Other more common UCA brands are Icon Vehicle Dynamics, Camburg, Total Chaos.

Beyond 3" of suspension lift, you will need to do more modifications.