unfortunately you found out the hard way that the spacer lift (especially when doing a full 3/2 spacer lift) is can over travel your suspension, especially when going off road. The spacer lift is affordable and good if you're just looking for a cosmetic lift and plan on keeping it on the pavement, but that's about it. Since you do some hunting and perhaps find yourself off road from time to time, i would definitely consider a true suspension lift.
Like gerdo mentioned, you should be able to address the situation with new shocks. If you have the money, i'm a big advocate of the ome suspension. My personal opinion is that the overland warehouse, icon, fox, etc. Adjustable coilovers are overkill (not to mention expensive) for what most people realistically use their 4runner for. Coming in comfortably south of $1k, the ome suspension will get you the lift you want in a true, off-road capable setup.
ome full suspension -- click here for details - toytec lifts: Toyota lift kits: Fj cruiser lift kits, tacoma lift kits, tundra lift kits, 4 runner lift kits, sequoia lift kits, toyota truck lift kits
at some point, i would also recommend the light racing uca's, but i would start by ditching the spacers. Best of luck.