Sleeping two people in a 3rd gen 4runner? Well, it's possible but I don't think I'd call it "comfortable."
I slept (1 person) in my 3rd gen and found it adequate but only just. Here's something you need to consider: When you travel, you have a lot of "stuff" (cooking gear, food, cooler or refrigerator, etc.) When you're driving that stuff is in the back of your truck. But where are you going to put it when you sleep? You cannot sleep 2 people inside a 3rd gen 4runner and have room left over for stuff - it's stuff or people, not both. Again, traveling by myself with a fairly minimal amount of gear I was barely able to sleep in my vehicle with all the stuff inside. When camping I normally set everything outside but if you are traveling in populated countries that's not an option.
I suppose you could build a platform but it would have to be a pretty high platform to accomodate a refrigerator or a cooler. And of course the higher you build your platform the less room you'll have above your head.
I'm not a huge fan of roof top tents but if you are planning on making a long trip with 2 people, that might be a good option. At least it will allow you to sleep off the ground and still have your stuff securely stored. RTT's are heavy and you will have to have a pretty substantial rack to carry one with 2 people in it, but I know there are 3rd gen 4runners that have used RTTs.
But that's only the interior - the other factor that you need to consider (and this is one of my biggest gripes, I always bring this up when talking about the 3rd gen 4runner) is the poor MPG and undersized fuel tank. It's not a big deal in most of the US and Canada or Western Europe but if you are planning on traveling outside of that region, you may want to see if you can either fab up an auxiliary tank (if you can relocate the spare tire to the back bumper, you'll have a space under the rear of the truck for a spare tank) or figure a way to carry several gas cans. The 18.5 gallon tank combined with the 11-15 MPG you can expect with a fully loaded vehicle hauling a RTT will give you maybe 200 miles range, max.
Of course, gasoline LCs also get terrible gas mileage but at least they have a 24 or 25 gallon tank to offset the range issue a little.
It sounds like you have both money and time to plan, I think I would try really hard to get a diesel LC. The LC is not only bigger, it's more of a "World platform" and the diesel model has a big gas tank + decent MPG.