Yes you can put OME coils over you stock shocks, but why would you? You entirely run the risk of doing permenent damage to your stock shocks and then you'll have to replace them anyway. I was advised by knowledgeable suspension mechanics that they have seen people do this coil swap out, and even if they don't off road, the stock shocks seperated causing lots of damage. Because of the 3" length difference, the stock shocks are not designed to go that length, and will pull apart. All it takes is one pot hole, one branch in the road, one accidently driven off curb.
Do what you want to your 4Runner, but to me the cost of buying 4 shocks over waiting for damage to occur just doesn't make sence. And because I love 4Runners and their reputation, I'd never want to see this happen. To me, do it right or don't do it at all. If you want a lift JUST for looks, go with the cornfed/daystar/roger brown whatever spacer lift. As trd-4Runnin says, the OME coil swap out will work, and I'm happy it's working for him and he's happy with it. But that's not they way the designers meant for the suspension to be used. Why stress parts out the wrong way? Do your own research that way you'll be ok with whatever you break down the road. The OME system was designed for off road use. Again, I think the spacer lift is what you are looking for. It's the cheapest way to get higher, & the easiest to put in and take out.