.........If you really wanted to you could do ball joint spacers, however i would not recommend this, they are not safe............
Not sure where you heard this, but I have been running a set on my '91 trail rig for over 10yrs now, w/o issue, other than the tearing if CV boots. The only thing that ball-joint spacers can do is cause bump steer, but that can be resolved by an alignment shop or tech that can do more than set things to factory specs.
92 4Runner.
Stock link suspension.
Are there any modifications I can do to get more flex?
besides taking off the sway bar 
For the rear, OOP's recommendation would be the best bet.
.............I have either 2" (I think) BJ spacers on the front now, and the torsion bars are cranked like a pregnant dog. 
For the front you could buy/make your own sway bar disconnect, but if the torsion bars are cranked for lift, disconnecting the sway bar wont do anything,
I have heard of people using the fj springs to lift their trucks or eliminate the ass-sag.. not sure if that would do the job but I could always try
The sag can be resolved with new different springs, spring spacers, or air bag helper springs which is the what a buddy is running in his 3rd gen Runner.
Gotta figure out how to get my tires to stop rubbing now, I have 35x12.5's and they rub when I'm at full lock. I cut the fender a good bit but it still rubs, maybe lowering the torsion bars a little will push the tires out some, and give me the little bit of clearance I need. Other than that, I will just havde to start cutting 
Taking a hammer to the firewall will clearance the tires some at full steering lock, but likely not enough to prevent rubbing. If it were me, I would install a 2" body lift, this will give you the clearance needed and will allow you to run the torsion bars at stock setting or lower, allowing the most flex out of the IFS, as well as steering clearance.
The 2" body lift will also allow you to raise the gas tank 2" increasing ground clearance and helping to reduce the "fuel capacity reducing dent" common to 4 Runners.
With the above mods and 2" removed from the fender on my '91, I have 1" or more at steering wheel lock, and about 3"of up travel in that position before the 35's(15x10 w/2" back spacing) will start to rub.
