well the vibration has come back... ugh
Just to add some additional, and probably more confusing, information to your equation:
I have a 2012 Trail Edition that came with Bridgestone Dueler H/T tires, possibly the worst, and most dangerous, tires I have ever had on a vehicle. I drove on them for 2-3k miles and then had them replaced. The vibration started with the OEM tires (Bridgestone Dueler H/Ts). It would happen on the highway right around 60-65 MPH and could be pretty intense. I took them back to the dealer and had them check the balance and alignment which they claimed were fine. Since I knew I was going to get rid of the tires anyway I just waited to see.
Well, I replaced the horrible Dueler tires with BFG Rugged Terrain T/As in stock size and went ahead and got MB Stryker wheels as well. The vibration was still there but it happened more around 65-70 MPH. So, after having Discount Tire balance them again twice, second time with the road force balancing, the vibration almost completely went away, just the occasional minor shudder on the highway. Now, four years later, the BFGs have close to 50k miles on them. While they still have some tread life left they are starting to get kind of chunked up around the edges. I run them at a consistent 32 PSI cold for a little softer ride so they wear a bit more to the outside. Anyway, the vibration had come back for the last 2k miles or so around 60-65 MPH, but not as intense as it was originally. Last week I had the Toytec Boss suspension kit and SPC Light Racing UCAs installed and that seemed to tighten up the front end quite a bit. So now, with the BFGs there is only the slightest vibration, again at around 60 MPH. The BFGs are getting replaced later this week with some new Cooper AT3s in C rated 275/70/17 size, so we will see what effect that has.
Bottom line, there are many variables that seem to come into play with this issue and tires, wheels and balancing play a big part in the overall ride quality. A heavier, stiffer suspension seems to make quite a bit of difference as well. I have to say I like the way the truck looks and feels quite a bit better with the new suspension anyway and wish I had done it a long time ago. I would personally stick with your existing vehicle if you still like it otherwise and try working on the tires and suspension to see if you can't get rid of the shakes. Of course, if you really would prefer the newer version and have the funds then go that route. Either way sticking with a 4Runner is the important thing, it is the best SUV on the market for the money easily.